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The Betta coccina complex is a diverse taxonomic group of fighting fish widely distributed in isolated islands in Southeast Asia. This genus is an ideal model for investigating freshwater fish evolutionary patterns and historical biogeography in the Malay Archipelago. In this study, based on principal component analysis of morphological traits, taxonomic diagnoses, and phylogenetic analysis of the mitochondrial cytochrome b gene, two new species are described from Sumatra Island, Betta iaspis sp. nov. and Betta mulyadii sp. nov. The former has a distinctive black anal fin with a few red patches on the posterior half, while the latter is red and unspotted throughout, distinguishing them with their five or six subdorsal scales from other members of the Betta coccina complex. Phylogenetic analysis of the Betta coccina complex based on Cyt b further suggests that the speciation and present distributional pattern of this complex cannot be explained simply by the current geographic isolation of the Strait of Malacca, but by the connection-isolation scenario in the Pleistocene biogeographic context in Sundaland. This metapopulation of extant Betta species suggests a potential radiative evolution before the Last Glacial Maximum. These findings advance our understanding of the taxonomy and biogeographic evolution of Betta species in Southeast Asia.