52．中島 淳・洲澤 譲・清水孝昭・斉藤憲治. 2012. 日本産シマドジョウ属魚類の標準和名の提唱. 魚雑 59:86-95.

51．Nakatani M, Miya M, Mabuchi K, Saitoh K, Nishida M. 2011. Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evol Biol 11:177.

50．Tang KL, Agnew MK, Chen W-J, Hirt MV, Raley ME, Sado T, Schneider LM, Yang L, Bart HL, He SP, Liu H, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL. 2011. Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). Mol Phylogenet Evol 61:103-124.

49．Saitoh K, Sado T, Doosey MH, Bart HLJr, Inoue JG, Nishida M, Mayden RL, Miya M. 2011. Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zool J Linn Soc 161:633-662.

48．Sekino M, Saitoh K, Shimizu D, Wada T, Kamiyama K, Gambe S, Chen S, Aritaki M. 2011. Genetic structure in species with shallow evolutionary lineages: a case study of the rare flatfish Verasper variegatus. Conserv Genet 12:139-159.

47．Kawamura K, Yonekura R, Ozaki Y, Katano O, Taniguchi Y, Saitoh K. 2010. The role of propagule pressure in the invasion success of bluegill sunfish, Lepomis macrochirus, in Japan. Mol Ecol 19:5371-5388.

46．Garvin MR, Saitoh K, Gharrett AJ. 2010. Application of single nucleotide polymorphisms in ecology: a technical review. Mol Ecol Resourc 10:915-934.

45．Tang KL, Agnew MK, Chen W-J, Hirt MV, Sado T, Schneider LM, Freyhof J, Sulaiman Z, Swartz E, Vidthayanon C, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL. 2010. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol 57:189-214.

44．Garvin MR, Saitoh K, Chrikov DY, Brykov VA, Gharrett AJ. 2010. Single nucleotide polymorphism in chum salmon (Oncorhynchus keta) mitochondrial DNA derived from restriction haplotype information. Genome 53:501-507.

43．Saitoh K, Chen W-J, Mayden RL. 2010. Extensive hybridization and tetrapolyploidy in spined loach fish. Mol Phylogenet Evol 56:1001-1010.

42．Doosey MH, Bart HLJr, Saitoh K, Miya M. 2010. Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences. Mol Phylogenet Evol 54:1028-1034.

41．Mayden RL, Chen W-J, Bart HL, Doosey MH, Simons AM, Tang KL, Wood RM, Agnew MK, Yang L, Hirt MV, Clements MD, Saitoh K, Sado T, Miya M, Nishida M. 2009. Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes - order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol 51:500-514.

40．Saitoh K, Uehara S, Tega T. 2009. Genetic identification of fish eggs collected in Sendai Bay and off Johban, Japan. Ichthyol Res 56:200-203.

39．Kawamura K, Yonekura R, Katano O, Taniguchi T, Saitoh K. 2009. Phylogeography of the bluegill sunfish, Lepomis macrochirus, in the Mississippi River Basin. Zool Sci 26:24-34.

38．Chen W-J, Miya M, Saitoh K, Mayden RL. 2008. Phylogenetic utility of two existing and four novel nuclear loci in reconstructing tree of life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as a case study. Gene 423:125-134.

37．Saitoh K, Chen W-J. 2008. Reducing cloning artifacts for recovery of allelic sequences by T7 endonuclease I cleavage and single re-extension of PCR products -- A benchmark. Gene 423:92-95.

36．Mayden RL, Tang KL, Wood RM, Chen W-J, Agnew M, Conway KW, Yang L, Simons AM, Bart HL, Harris PM, Li J, Wang Z, Saitoh K, He S, Liu H, Chen Y, Nishida M, Miya M. 2008. Inferring the tree of life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling. J Syst Evol 46:424-438.

35．Sekino M, Saitoh K, Aritaki M. 2008. Microsatellite markers for a rare species of right-eye flounder Verasper variegatus (Pleuronectiformes, Pleuronectidae). Conserv Genet 9:761-765.

34．Mayden RL, Tang KL, Conway KW, Freyhof J, Chamberlain J, Haskins M, Schneider L, Sudkamp M, Wood RM, Agnew M, Bufalino A, Sulaiman Z, Miya M, Saitoh K, He S. 2007. Phylogenetic relationships of Danio within the order Cypriniformes: A framework for comparative and evolutionary studies of a model species. J Exp Zool 308B:642-654.

33．Shigenobu Y, Hayashizaki K, Asahida T, Ida H, Saitoh K. 2007. Stock structure of Japanese flounder inferred from morphological and genetic analyses. Fish Sci 73:1104-1112.

32．Lavoue S, Miya M, Saitoh K, Ishiguro NB, Nishida M. 2007. Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences. Mol Phylogenet Evol 43:1096-1105.

31．Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M. 2006. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826-841.

30．Saitoh K, Muraoka D. 2006. Undaria mitochondrial large subunit ribosomal DNAs (Phaeophyceae, Alariaceae): Structural properties and use for phylogenetic analysis. Phycol Res 54:149-153.

29．Miya M, Saitoh K, Wood R, Nishida M, Mayden RL. 2006. New primers for amplifying and sequencing the mitochondrial ND4/ND5 gene region of the Cypriniformes (Actinopterygii: Ostariophysi). Ichthyol Res 53:75-81.

28．Kawamura K, Yonekura R, Katano O, Taniguchi Y, Saitoh K. 2006. Origin and dispersal of bluegill sunfish, Lepomis macrochirus, in Japan and Korea. Mol Ecol 15:613-621.

27．Muraoka D, Saitoh K. 2005. Identification of Undaria pinnatifida and Undaria undarioides (Laminariales, Phaeophyceae) using mitochondrial 23S ribosomal DNA sequences. Fish Sci 71:1365-1369.

26．Shigenobu Y, Saitoh K, Hayashizaki K, Ida H. 2005. Nonsynonymous site heteroplasmy in fish mitochondrial DNA. Gene Genet Syst 80:297-301.

25．Lavoue S, Miya M, Inoue JG, Saitoh K, Ishiguro NB, Nishida M. 2005. Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala. Mol Phylogenet Evol 37:165-177.

24．Sekino M, Saitoh K, Yamada T, Hara M, Yamashita Y. 2005. Genetic tagging of released Japanese flounder (Paralichthys olivaceus) based on polymorphic DNA markers. Aquaculture 244:49-61.

23．Asahida T, Shinotsuka Y, Saitoh K, Tsuzuki T, Aritaki M, Yamashita Y. 2004. Parental contributions in a Japanese flounder hatchery inferred from mitochondrial DNA haplotypes. J World Aquacult Soc 35:199-208.

22．Saitoh K, Kim I-S, Lee E-H. 2004. Mitochondrial gene introgression between spined loaches via hybridogenesis. Zool Sci 21:795-798.

21．Saitoh K. 2003. Mitotic and meiotic analyses of the 'large race' of Cobitis striata, a polyploid spined loach of hybrid origin. Folia Biol (Krakow) 51(Suppl):101-105.

20．Asahida T, Shinotsuka Y, Yamashita Y, Saitoh K, Hayashizaki K, Ida H. 2003. Influence of hatchery protocols on mitochondrial DNA variation in Japanese flounder juveniles. J World Aquacult Soc 34:121-132.

19．Sekino M, Saitoh K, Yamada T, Kumagai A, Hara M, Yamashita Y. 2003. Microsatellite-based pedigree tracing in a Japanese flounder Paralichthys olivaceus hatchery strain: implications for hatchery management related to stock enhancement program. Aquaculture 221:255-263.

18．Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M. 2003. Mitochondrial genomics of ostariophysan fishes: Perspectives on phylogeny and biogeography. J Mol Evol 56:464-472.

17．Saitoh K, Takagaki M, Yamashita Y. 2003. Detection of Japanese flounder-specific DNAs from gut contents of potential predators in the field. Fish Sci 69:473-477.

16．斉藤憲治. 2003. 農業土木技術者のための生き物調査（その７）─淡水魚調査法─. 農土誌 71:241-245.

15．Kawamura K, Ueda T, Arai R, Nagata Y, Saitoh K, Ohtaka H, Kanoh Y. 2001. Genetic introgression by the rose bitterling, Rhodeus ocellatus ocellatus, into the Japanese rose bitterling, R. o. kurumeus (Teleostei: Cyprinidae). Zool Sci 18:1027-1039.

14．Saitoh K, Kobayashi T, Ueshima R, Numachi K. 2000. Analyses of mitochondrial and satellite DNAs on spined loaches of the genus Cobitis from Japan have revealed relationships among populations of three diploid-tetraploid complexes. Folia Zool 49(S1):9-16.

13．Saitoh K, Ueda T, Arai R, Wu H-L, Jeon S-R. 2000. Highly repetitive elements from Chinese bitterlings (genus Rhodeus, Cyprinidae). Gene Genet Syst 75:349-355.

12．Saitoh K, Hayashizaki K, Yokoyama Y, Asahida T, Toyohara H, Yamashita Y. 2000. Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships. J Hered 91:271-278.

11．Saitoh K. 1998. Genetic variation and local differentiation in the Pacific cod Gadus macrocephalus around Japan reveald by mtDNA and RAPD markers. Fish Sci 64:673-679.

10．朝日田 卓・斉藤憲治・山下 洋・青沼佳方・小林敬典. 1998. ミトコンドリアＤＮＡの制限酵素切断型によるヒラメ天然集団の遺伝的変異. 日水誌 64:377-383.

９．Asahida T, Kobayashi T, Saitoh K, Nakayama I. 1996. Tissue preservation and total DNA extraction from fish stored at ambient temperature using buffers containing high concentration of urea. Fish Sci 62:727-730.

８．Saitoh K, Tanaka M, Ueshima R, Kamaishi T, Kobayashi T, Numachi K. 1995. Preliminary data on restriction mapping and detection of length variation in Japanese flounder mitochondrial DNA. Aquaculture 136:109-116.

７．Saitoh K. 1990. Reproductive and habitat isolation between two populations of the striated spined loach. Env Biol Fish 28:237-248.

６．Saitoh K. 1989. Multiple sex chromosome system in a loach fish. Cytogenet Cell Genet 52:62-64.

５．斉藤憲治・藤川博史・長田芳和. 1988. 島根県大田市大原川から採集されたアカヒレタビラ. 日生地学報 43:57-60.

４．片野修・斉藤憲治・小泉顕雄. 1988. ナマズ Silurus asotus のばらまき型産卵行動. 魚雑 35:203-211.

３．斉藤憲治・片野 修・小泉顕雄. 1988. 淡水魚の水田周辺における一時的水域への侵入と産卵. 日生誌 38:35-47.

２．Saitoh K, Aizawa H. 1987. Local differentiation within the striated spined loach (the striata type of Cobitis taenia complex). Jpn J Ichthyol 34:334-345.

４．村岡大祐・斉藤憲治. 2006. 褐藻ワカメ類の塩基配列情報を用いた種判別, pp112-120, 福田 裕・渡部終五・中村弘ニ（編）, 水産学シリーズ149　水産物の原料・原産地判別技術, 恒星社厚生閣, 東京.

３．斉藤憲治. 2005. スジシマドジョウ種群─高密度なのに，実は稀少魚─, pp186-192, 片野 修・森 誠一（編）, 稀少淡水魚の現在と未来─積極的保全のシナリオ─, 信山社, 東京.

２．斉藤憲治. 1997. 淡水魚の繁殖場所としての一時的水域, pp194-204, 長田芳和 ・細谷和海（編）, 日本の希少淡水魚の現状と系統保存, 緑書房, 東京.

18. 大原一郎・星野浩一・高嶋康晴・小林敬典・斉藤憲治・重信裕哉・猿渡敏郎・米沢純爾. 2011. Site-specific PCR を用いたハマトビウオ属6種の種判別. DNA多型 19:110-114.

17. 斉藤憲治. 2010. マグロゲノム解読プロジェクトの紹介. 日水誌 76:1132-1134.

16. 大原一郎・星野浩一・高嶋康晴・小林敬典・斉藤憲治・重信裕哉・猿渡敏郎. 2010. Site-specific PCR を用いたムロアジ属6種の種判別. DNA多型 18:98-101.

15. Tanaka N, Akaike S, Ishii M, Ishikawa R, Ito H, Kudo T, Muraoka D, Oshino A, Saigusa M, Urabe S, Yatsuya K, Morita K, Saitoh K. 2009. Distribution of Zostera species in Japan. II Zostera asiatica Miki, Z. caespitosa Miki and Z. caulescens Miki (Zosteraceae). Bull Natl Mus Nat Sci [B] 35:211-218.

14. Tanaka N, Aida S, Akaike S, Aramaki H, Chiyokubo T, Chow S, Fujii A, Fujiwara M, Ikeuchi H, Ishii M, Ishikawa R, Ito H, Kudo T, Muraoka D, Nagahama T, Nambu T, Okumura H, Oshino A, Saigusa M, Shimizu Y, Suwa T, Suzuki K, Takeda K, Tanada N, Tanimoto T, Tsuda F, Urabe S, Yatsuya K, Yoshida G, Yoshimatsu T, Yoshimitsu S, Yoshimura K, Morita K, Saitoh K. 2009. Distribution of Zostera species in Japan. I Zostera marina L. (Zosteraceae). Bull Natl Mus Nat Sci [B] 35:23-40.

13. 斉藤憲治・川岸基能・進東健太郎. 2007. 宮城県名取川水系産のアカヒレタビラの搾出完熟卵は細長く稚魚の背びれには黒斑がない. 伊豆沼・内沼研究報告 1:1-5.

12．斉藤憲治. 2003. 木村英造「淡水魚にかける夢」上野敏彦. 2003. 平凡社, 東京. 358pp, ISBN4-582-83158-3. 2400円（税別）. 魚雑 50:169（書評）.

11．東 幹夫・斉藤憲治・片野 修. 2002. 魚類の調査方法 (2) モンドリによる淡水魚の採捕. 魚雑 49:158-160.

10．斉藤憲治. 2002. 研究会紹介ﾑ第34回魚類自然史研究会. 魚雑 49:154-156.

９．斉藤憲治. 2002. 「世界の淡水魚の自然史」という本の1つの理想形 "Freshwater Fish Distribution" T.M. Berra. 2001. Academic Press, San Diego. xxxviii+604pp. ISBN0-12-093156-7. 魚雑 49:59（書評）.

８．Saitoh K, Kobayashi T, Asahida T, Hayashizaki K, Yokoyama Y, Toyohara H, Yamashita Y. 2001. Sequence and structure of Japanese flounder (Paralichthys olivaceus) mitochondrial genome. Bull Tohoku Natl Fish Res Inst 64:1-36.

７．Saitoh K. 2000. Sumio Minamori: the pioneer of loach speciation study. Folia Zool 49(S1):249-252.

６．Saitoh K, Bohlen J, Rab P. 2000. Preface. Folia Zool 49(S1):2.

５．Mizuno M, Kobayashi T, Matsuishi T, Maeda K, Saitoh K. 2000. Stock structure of walleye pollock, Theragra chalcogramma, around Hokkaido and Sakhalin in the term of mitochondrial DNA RFLP. Sci Rep Hokkaido Fish Exp Stn 57:1-8.

４．斉藤憲治. 1993. スジシマドジョウ小型種と大型種の急減. 魚雑 40:394-397.

３．斉藤憲治・松田征也. 1990. 琵琶湖水系に分布するシマドジョウ類. 滋賀県立琵琶湖文化館研究紀要 8:19-23.

２．松田征也・斉藤憲治. 1989. 日本産ヒナモロコ Aphyocypris chinensis Gunther の染色体. 滋賀県立琵琶湖文化館研究紀要 7:21-23.