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Allozyme electrophoresis was used to investigate stock integrity of Patella aspera (= P. ulyssiponensis) and Patella candei (Mollusca, Patellogastropoda) from the Madeira Archipelago. Samples from the north of the island of Madeira (Porto Moniz) and the north of Deserts Grande were taken for both species, and a sample of P. aspera was also taken from the south of the island of Madeira (Canico). Twenty-one putative loci were resolved and analyzed for both species. Significant differences in allele frequencies were found between locations in each species. suggesting the presence of different genetic stocks. P. candei was found to be slightly structured with a small standardized variance in allele frequencies between samples from Porto Moniz and Deserta Grande (F-ST = 0.036); whereas, P. aspera was highly structured, with an F-ST value over all subpopulations of 0.157. Our results indicate more genetic interchange between the populations from the north of Madeira and Deserta Grande than between north and south Madeira. Our findings are consistent with surface water-mass circulation patterns from northwest to southeast along the Madeira Archipelago, determined mainly by the Canary Current. Species with low dispersal and a high degree of spatial genetic structuring among subpopulations are more susceptible to collapse caused by over fishing than those with high dispersal capabilities; therefore, the individual management and control of these biological units is recommended.