The design of appropriate management plans of the green abalone Haliotis fulgens fishery needs a better understanding of the present status of the genetic diversity of the wild stock, as well as its genetic structure. Samples from nine locations along the Baja California Peninsula, including one from an oceanic island (Isla Guadalupe), were obtained covering the areas where the commercial fishery is active. DNA was extracted from muscle tissue of 50 individuals from each location, and was used for PCR amplification of 4 microsatellites (Hka28, Hka56, Hful260, and Hful603). The number of alleles observed in all samples with Hka28 and Hka56 (23–35 and 15–19, respectively) was higher than that observed in Hful260, and Hful603 (3 and 6 alleles, respectively). A relatively high mean heterozygosity was observed in all locations with the lowest value of 0.687 in Isla Guadalupe. A deviation from Hardy-Weinberg Equilibrium (HWE) caused by a heterozygote deficiency was only observed in 2 out of 36 tests, indicating that this disequilibrium is random. An AMOVA showed a significant F_ST (P < 0.00196) suggesting genetic differentiation among locations. Pairwise analyses using F_ST and allele frequencies showed that the significant difference was caused by Isla Guadalupe, which indicates a restricted gene flow between this and the other locations. Nevertheless, no significant differences were observed among sites along the Peninsula. The implications of these results on the management of the fishery are discussed.