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The air sac catfish, Heteropneustes fossilis (Siluriformes: Heteropneustidae), is widely distributed in freshwaters of the Indian subcontinent and mainland southeast Asia. No comprehensive molecular studies that cover the broad distributional areas have been carried out to date. Here, we conducted molecular phylogenetic analyses using both mitochondrial and nuclear gene sequences to suggest that the Heteropneustes fossilis species complex consists of three clades that may potentially be separate species with distinct geographical distribution (southeast Asia, northeastern India, and southwestern India). The first and second clades are more closely related to each other than they are to the third clade. Within the first clade there is a basal divergence of a subclade consisting of individuals from the Upper Irrawaddy River basin of Myanmar, which share some morphological traits with members of the Indian clades. Our molecular and morphological data are congruent with hypotheses that the Early-Middle Miocene disconnection between the paleo-Tsangpo River and the Irrawaddy River caused the vicariant divergence between southeast Asian and northeastern Indian clades, and that the southeast Asian Heteropneustes originated from the Upper Irrawaddy.

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