The genus Corbicula is well known as one of the most invasive bivalves globally, and is morphologically variable and taxonomically complicated. Continuous effort has been made to establish the correspondence between morphological forms and genetic lineages of Corbicula, mostly across invasive populations, but far less for the native populations, especially for exploited ones that support important Corbicula fishery. This research studied a Corbicula population that supported the largest artisanal and commercial Corbicula fishery in China, in terms of the morphotypes composition, ploidy, mt COI sequence, phylogenetic relationship, and habitat preferences. Two morphotypes with 9.5% mt COI genetic divergence, that is, the “distantly-placed-ridges morphotype”-morph D, and the “closely-situated-ridges morphotype”-morph C were identified. Morph D individuals contained diploids and triploids, and were closely related to the invasive lineage. They were found in higher proportions in lotic habitats with lower transparency and chlorophyll α. Morph C were all diploids and sister to C. fluminalis and C. japonica. They had higher proportions in lentic habitats. Thus, fishery management of Corbicula should consider multiple compositions of the Corbicula resource. Further research that confirms the population parameters difference of the two morphotypes and surveys in other water systems should be conducted. Moreover, the two morphotypes were sympatric representatives of the invasive and noninvasive Corbicula lineages, comparisons between them and with their congener invasion populations suggested that preference of flowing water and polyploidy might contribute to the invasive success of some Corbicula lineages in addition to androgenesis.