Single nucleotide polymorphisms (SNPs) are rapidly becoming the population genomic markers in addressing ecology, evolution, and conservation issues for their high capacity to access variability across the genome. We isolated a total of 140 ideal SNPs from the finless porpoise and used 78 (under Hardy–Weinberg equilibrium) of them to conduct those issues especially for addressing population genetic differentiation. Bayesian clustering and principal component analyses all suggested that finless porpoises in Chinese waters could be divided into three distinct genetic groupings. Low levels of within-population genetic variation (mean HE = 0.3405, standard deviation = 0.1188) and significant differentiation among populations (FST = 0.1050–0.1628, P < 0.01) were confirmed. Limited gene flow was found especially between the freshwater Yangtze River porpoise and the oceanic Yellow Sea and South China Sea populations, which strongly suggested that some barriers might have restricted their genetic exchange. These evidences not only support a recent subdivision of the finless porpoise into two species but also suggest a full species status for the Yangtze finless porpoise, especially considering the significant genetic divergence between freshwater and marine porpoises, in combination with the unique distribution of Yangtze finless porpoises in freshwater and their distinctness in physiological and morphological features.