The sea urchin Paracentrotus lividus is the most commercially important sea urchin species harvested in the NE Atlantic and Mediterranean coasts. To improve the management of P. lividus natural stock and its commercial exploitation, the population genetic structure of P. lividus in the Northeast Atlantic coast has been characterized. Populations from three regions of Spain: Asturias, Galicia, and the Canary Islands were sampled, and a 700-bp fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) was sequenced. The obtained sequences were combined with previously available haplotypes coming from 127 sea urchins from the Canary Islands and the Mediterranean and Atlantic coasts of Spain—they collapsed in 54 haplotypes with 43 polymorphic sites—and 13 of these haplotypes were provided for the obtained sequences. The haplotype network shows high haplotype diversity and low nucleotide diversity values in all the studied populations. The distribution of analyzed haplotypes shows a high genetic homogeneity among populations. With the obtained data, no significant genetic differentiation could be found among populations analyzed in Galicia, Asturias, and the Canary Islands, and the existence of a population structure in this geographical area could not be determined. Based on this study, there would be no loss of genetic variability if the shores of the Canary Islands were repopulated with urchins from the Iberian Peninsula, although it is recommended to repopulate overexploited areas with urchins from the same zone until the study is extended with other molecular markers.