Several cetacean species are endemically distributed throughout the Indo-Pacific. Due to disproportionate sampling and research efforts across the Indo-Pacific region, the spatial genetic structure of these species remains poorly understood. This has led to poor phylogeographic knowledge and ambiguous taxonomic classification of many Indo-Pacific cetacean species. Of these, the finless porpoise (genus Neophocaena) is a small cetacean obligatory to the inshore waters from East Asia to the Persian Gulf of the Indian Ocean. To date, two species are generally recognized: the narrow-ridged finless porpoise inhabiting temperate and subtropical waters, and wideridged finless porpoises inhabiting subtropical and tropical waters. Early research efforts focused on the temperate waters off the northern China. However, recent studies have proposed that the primary divergence within the genus may lie between the Indian Ocean and Pacific region, which remains to be tested with more samples from tropical and subtropical regions. Here, we examined the genetic relationship among the finless porpoises from the Gulf of Thailand to the Taiwan Strait using both mitochondrial and autosomal markers. Bayesian assignment analysis suggested a minimum of four genetic populations within the study areas, corresponding to the narrowridged finless porpoise from the Taiwan Strait (TWSn), and the three wide-ridged finless porpoise populations from the Taiwan Strait (TWSw), Pearl River Delta region (PRDw), and the Gulf of Thailand (Thaiw), respectively. The minimum spanning network of the mtDNA control region found shared haplotypes among finless porpoises in Chinese waters, but those from the Gulf of Thailand formed a unique matriline lineage. Consistently, the genetic differentiation or divergence within the South China Sea (Thaiw vs. PRDw) appears to be higher than that of most finless porpoise populations examined to date, and meets the threshold values of species or sub-species level proposed for the cetacean species. The Mantel test detected a strong correlation between the geographic and genetic matrices within the South China Sea (r > 0.99, p < 0.001), indicating that the divergence associated with isolation-by-distance (IBD) has been accumulating in recent history. Our results imply that the formation and maintenance of the spatial genetic pattern of the finless porpoise is more complex than previously thought. However, this cannot be addressed by the current taxonomic classification of the genus.