1979

• Matsui, M. 1979: Amphibians from Sabah I. Systematic and natural history notes. Contributions from the Biological Laboratory, Kyoto University, 25: 303–346.

1984

• Matsui, M. 1984: Morphometric variation analyses and revision of the Japanese toads (Genus Bufo, Bufonidae). Contributions from the Biological Laboratory, Kyoto University, 26: 209–428.

1990

• Matsui, T. & Matsui, M. 1990. A new brown frog (genus Rana) from Honshu, Japan. Herpetologica 46(1): 78–85. JSTOR. Reference page. 

1994

• Matsui, M. 1994: A taxonomic study of the Rana narina complex, with description of three new species (Amphibia: Ranidae). Zoological Journal of the Linnean Society, 111: 385–415.

1997

• Matsui, M. 1997: Call characteristics of Malaysian Leptolalax with a description of two new species (Anura: Pelobatidae). Copeia, 1997: 158–165.

2011

• Nishikawa, K., Jiang, J.-P., Matsui, M. & Mo, Y.-M. 2011. Unmasking Pachytriton labiatus (Amphibia: Urodela: Salamandridae), with description of a new species of Pachytriton from Guangxi, China. Zoological Science 28(6): 453–461. DOI: 10.2108/zsj.28.453 Reference page. 

2012

• Matsui, M. (manuscript April 2012): Leptolalax Zootaxa,
• Matsui Masafumi; Hamidy Amir; Murphy Robert W; Khonsue Wichase; Yambun Paul; Shimada Tomohiko; Ahmad Norhayati; Belabut Daicus M; Jiang Jian-Ping. Phylogenetic relationships of megophryid frogs of the genus Leptobrachium (Amphibia, Anura) as revealed by mtDNA gene sequences.
• Kotaki Manabu; Kurabayashi Atsushi; Matsui Masafumi; Kuramoto Mitsuru; Djong Tjong Hon; Sumida Masayuki. Molecular phylogeny of the diversified frogs of genus fejervarya (anura: dicroglossidae).
• Yoshikawa Natsuhiko; Matsui Masafumi; Nishikawa Kanto. Allozymic variation and phylogeography of two genetic types of Onychodactylus japonicus (Amphibia: Caudata: Hynobiidae) sympatric in the Kinki District, Japan.
• Matsui, M. 2009. A New Species of Philautus (Amphibia, Anura, Rhacophoridae) from the Lowland of Sarawak, Western Borneo. Zoological Science. Tokyo 26: 437–442.

2014

• Matsui, M. & Nishikawa, K. 2014. Description of a new species of Limnonectes from Sarawak, Malaysian Borneo (Dicroglossidae, Anura). Current Herpetology 33(2): 135–147. DOI: 10.5358/hsj.33.135 Reference page. 

• Nguyen, T.T., Matsui, M. & Duc, H.M. 2014. A new tree frog of the genus Kurixalus (Anura: Rhacophoridae) from Vietnam. Current Herpetology 33(2): 101–111. DOI: 10.5358/hsj.33.101 Reference page. 

• Nguyen, T.T., Matsui, M. & Eto, K. 2014. A new cryptic tree frog species allied to Kurixalus banaensis (Anura: Rhacophoridae) from Vietnam. Russian Journal of Herpetology 21(4): 295–302. Reference page. 

2017

• Kurita, T., Nishikawa, K., Matsui, M. & Hikida, T. 2017. A new species of Rock Gecko genus Cnemaspis (Squamata: Gekkonidae) from Western Sarawak, Malaysia. Zootaxa 4258(5): 525–538. DOI: 10.11646/zootaxa.4258.5.2 . Reference page. 

• Matsui, M., Eto, K., Nishikawa, K., Hamidy, A., Belabut, D., Ahmad, N., Panha, S., Khonsue, W. & Grismer, L.L. 2017. Mitochondrial phylogeny of Leptolalax From Malay Peninsula and Leptobrachella (Anura, Megophryidae). Current Herpetology 36(1): 11–21. DOI: 10.5358/hsj.36.11 Reference page. 

• Matsui, M., Ohler, A., Eto, K. & Nguyen, T.T. 2017. Distinction of Gracixalus carinensis from Vietnam and Myanmar, with description of a new species. Alytes 33(1-4): 25–37. Full article (PDF). Reference page. 

• Matsui, M., Nishikawa, K., Eto, K. & Hossman, M.Y.B. 2017. A new species of Pelophryne from western Sarawak, Malaysian Borneo (Anura, Bufonidae). Zoological Science 34(4): 345–350. DOI: 10.2108/zs170008 Reference page. 

• Matsui, M., Eto, K., Belabut, D.M. & Nishikawa, K. 2017. A new Kalophrynus (Amphibia, Anura, Microhylidae) from Peninsular Malaysia. Current Herpetology 36(2): 75–86. DOI: 10.5358/hsj.36.75 Reference page. 

• Matsui, M., Misawa, Y., Nishikawa, K. & Shimada, T. 2017. A new species of lentic breeding salamander (Amphibia, Caudata) from central Japan. Current Herpetology 36(2): 116–126. DOI: 10.5358/hsj.36.116 Reference page. 

• Matsui, M., Nishikawa, K. & Tominaga, A. 2017. Taxonomic relationships of Hynobius stejnegeri and H. yatsui, with description of the Amber-Colored Salamander from Kyushu, Japan (Amphibia: Caudata). Zoological Science 34(6): 538–545. DOI: 10.2108/zs170038 Reference page. 

2018

• Matsui, M., Khonsue, W. & Panha, S. 2018. Two New Species of Ansonia from Thailand (Anura: Bufonidae). Zoological Science 35(1): 39–48. DOI: 10.2108/ZS170120 . PubMed Reference page. 

• Atmaja, V.Y., Hamidy, A., Arisuryanti, T., Matsui, M. & Smith, E.N. 2018. A New Species of Microhyla (Anura: Microhylidae) from Sumatra, Indonesia. Treubia 45: 25–46. Reference page.