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Background  Sri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western ‘wet zone’. The island’s freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of  Pethia  ( P. bandula ,  P. cumingii ,  P. melanomaculata ,  P. nigrofasciata ,  P. reval ), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka.    Results  The phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan  Pethia  as polyphyletic. The reciprocal monophyly of  P. bandula  and  P. nigrofasciata , and  P. cumingii  and  P. reval , is not supported.  Pethia nigrofasciata ,  P. cumingii , and  P. reval  show strong phylogeographic structure in the wet zone, compared with  P. melanomaculata , which ranges across the dry and intermediate zones. Translocated populations of  P. nigrofasciata  and  P. reval  in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of  P. nigrofasciata  proximal to  P. bandula , a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of  P. cumingii  in the Kalu basin possess orange fins, a state between the red-finned  P. reval  from Kelani to Deduru and yellow-finned  P. cumingii  from Bentara to Gin basins.    Conclusions  Polyphyly in Sri Lankan  Pethia  suggests two or three colonizations from mainland India. Strong phylogeographic structure in  P. nigrofasciata ,  P. cumingii  and  P. reval , compared with  P. melanomaculata , supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between  P. bandula  and  P. nigrofasciata , and  P. cumingii  and  P. reval , and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12862-021-01923-5.

Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka