The finless porpoise (genus Neophocaena) is a poorly known cetacean of great conservation concern. Within its range, from western Pacific to northwestern Indian Ocean, there are currently two species recognized (N. asiaeorientalis and N. phocaenoides), thought to be reproductively isolated since last glacial maximum, with the only sympatric overlap zone in Taiwan Strait. However, the genetic variation across the genus’ distribution has not yet been extensively studied, especially in the Indian Ocean. We performed an exhaustive review of molecular data of the finless porpoise across its range. Neighbor-net networks analyses based on two mitochondrial loci (control region/CR and cytochrome b/cyt b) suggest that finless porpoises from the Indian and Pacific Ocean constitute two distinct clades, well-defined by fixed mutations at both loci. A molecular clock analyses indicate early split (CR: 13.1 Ma, cyt b: 12.9 Ma) between these two oceanic lineages, while spatial genetic analyses further suggest that in the Pacific the divergence was primarily due to the taxon from Japanese waters rather than inter-species divergence across the Taiwan Strait. As extinction risks can be substantially underestimated if threatened species are pooled together with non-threatened, especially in the absence of long-distance migration, we suggest that the present 2-species taxonomy of the genus Neophocaena should be given further examination, with concerted sampling effort in the Western Indian Ocean. More research effort and genomic information is needed before taxonomic revisions can be considered; such further studies are strongly recommended as they may affect the current status classification of the species constituting the genus Neophocaena. Most notably, the narrow-ridged finless porpoise off Japan merits urgent conservation attention.