The freshwater snail Indoplanorbis exustus play an important role as the sole intermediate host of several medically- and economically-important trematodes, especially zoonotic schistosomes and echinostomes, which can infect and cause diseases in livestock and people. This study aims to explore the mitochondrial cytochrome c oxidase subunit 1 sequence variation of I. exustus collected from new geographical areas; 459 specimens of I. exustus were collected from 43 localities in South and Southeast Asia. The 42 haplotypes (Ie1 - Ie42) we detected were classified into haplogroups I - V. Phylogenetic analyses revealed five major clades, A - E, in concordance with all previous studies. Clade E contained two subclades, E1 (haplogroup I) and E2 (haplogroup II). The most widespread genetic group was subclade E1. Clade A, clade B (haplogroup V), and clade C (haplogroup IV) were found only in South Asia, whereas clade D (haplogroup III) was specifically found in Southeast Asia. In Thailand, I. exustus showed high genetic divergence with 21 haplotypes. Several isolates showed significant genetic differences from others with unique haplotype(s). Hence, we confidently conclude our findings support all previous studies that I. exustus is a species complex with at least four major lineages and five haplogroups. Our additional analyses of 35 samples from Sri Lanka showed these were indeed an independent genetic group as previously found, but they can now be classified as a unique group forming subclade E2 (haplogroup II) of I. exustus sensu lato.