We compared mitochondrial genetic data for two spiny lobsters in Hawaii with different geographic ranges and histories of fishing pressure. Panulirus marginatus (Quoy and Gaimard, 1825) is endemic to Hawaii, and experienced a short, intense fishery in the Northwestern Hawaiian Islands (NWHI) and long-term, less intense exploitation in the Main Hawaiian Islands (MHI). Populations show significant overall structure (F ST = 0.0037, P = 0.007; D est_Chao = 0.137), with regional differentiation (F CT = 0.002, P = 0.047) between the MHI and the NWHI. Haplotype diversity did not differ significantly between regions (F2, 8 = 3.740, P = 0.071); however, nucleotide diversity is significantly higher at the primary NWHI fishery banks (0.030) than in the MHI (0.026, Tukey's P = 0.013). In contrast, Panulirus penicillatus (Olivier, 1791), found across the tropical Indo-West Pacific region, was not targeted by the NWHI fishery, but has experienced long-term exploitation in the MHI. Panulirus penicillatus has no significant overall population structure in Hawaii (F ST = 0.0083, P = 0.063; D est_Chao = 0.278), although regional differentiation (F CT = 0.0076, P = 0.0083) between the MHI and the NHWI is significant. Neither haplotype nor nucleotide diversity differed significantly between regions for P. penicillatus While neither species has suffered a loss of genetic diversity from fishing, our results highlight that only by incorporating knowledge of fishing history with genetic connectivity data can we understand the most beneficial management strategy for each species. Neither exemplar species nor specific suites of traits are reliable predictors of the spatial scales of management.