The mitochondrial cytochrome c oxidase subunit I gene (COI) was partially sequenced in specimens of the wild-type small abalone, Haliotis diversicolor, from Taiwan and Japan. There were a total of six wild-type populations with 153 individuals. Two populations from Taiwan, including 20 P (Penghu) and 11 H (Hualien), and 4 populations from Japan, including 20 N (Osaka), 18 M (Fukuoka), 38 D (Okinawa) and 46 JO (Shizuoka), were analyzed. The partial DNA sequence analysis from 835~838 base pairs of the COI gene identified the following 113 haplotypes: 19 (P) and 11 (H) haplotypes from Taiwan and 19 (N), 18 (M), 38 (D) and 33 (JO) from Japan. The variable sites of the two Taiwanese populations (3.95% in P and 4.78% in H) were lower than the four Japanese populations (6.71% in N, 19.59% in M, 11.69% in JO and 30.06% in D). The nucleotide diversity indexes (θπ) were 0.0051 (P) and 0.0093 (N) from the Taiwanese populations and 0.0101 (JO), 0.0123 (H), 0.0312 (M) and 0.0816 (D) from the Japanese populations. The haplotype analysis showed that the wild-type small abalone population in Taiwan was significantly lower than the wild-type small abalone population in Japan, suggesting a decrease in the genetic variation of the Taiwanese wild-type population.