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Recent speciation events provide important insights into the understanding and conservation of Earth's biodiversity, representing recent adaptations to a changing environment and an important source of future evolutionary potential. However, the most frequently applied criterion for molecular-based speciation investigations, that of reciprocal monophyly of mitochondrial sequences, overlooks recent speciation events where insufficient time has passed for fixed molecular differences to develop between putative species. Two morphologically distinguishable forms of finless porpoise (genus Neophocaena) exist in sympatry in the strait of Taiwan, however the taxonomic relationship of these different forms is controversial. To test the hypothesis that the two forms represent different species, a study was conducted based on morphological characters and microsatellite and mitochondrial markers. The data suggest that the two forms are highly differentiated in terms of both morphology and genetic characteristics, despite being sympatric, and therefore represent different species as defined by the biological species concept. Moreover, the two forms appear to have been reproductively isolated since sharing a common ancestor prior to the last major glaciation event approximately 18 000 years ago. However, this represents an insufficient amount of time for reciprocal monophyly to have developed, and thus previous studies based on this criterion have overlooked this speciation event and resulted in incorrect taxonomic classification of these forms.