Management plans and stock assessment of exploited marine invertebrates should consider information on the genetic population structure of the species. In this context, the genetic diversity within and between populations of the commercially exploited hairy edible crab Cancer setosus was investigated using allozyme and AFLP (Amplified Fragment Length Polymorphism) markers, covering a range of approximately 2500 km along the Chilean coast. Genetic diversity estimates within populations, such as polymorphism and average expected heterozygosity, were low from two polymorphic allozyme loci, PGM-1 and EST-1 (P_0.99 = 8.7 %; H_E = 2.5 %) but much higher for 190 AFLP loci (P_0.99 = 52 %; H_E = 18.7 %). Nevertheless, differentiation among samples was statistically significant for allozymes (F_ST = 0.026; P < 0.001), but not for AFLPs (AMOVA ϕ_PT = 0.007; P = 0.118). Several possible causes of these differences are discussed in an evolutionary and oceanographic framework. AFLP also identified a sex-linked marker, present in 96 % of females but only 9 % of males. Relatively little is known about sex-determination in decapods, but these data suggest that in C. setosus, the mechanism is primarily genetic and that females may be the heterogametic sex.