This dataset contains genetic diversity estimates from animals and plants occurring in the Mediterranean, spanning a period of over 30 years, from 1979 to 2010. Information was compiled from published scientific articles and personal communications of authors. The 9305 data points encompass 244 species, each characterized by its life history traits and its taxonomic classification. Data are at population level, for up to eight genetic markers per population, with microsatellites and allozymes being more than 2/3 of the data. Allelic richness and heterozygosity (both observed and expected) are the most frequent genetic diversity estimates reported. Each of the 3820 populations is identified by its geographic coordinates and its paleoclimate 21,000 years ago. The data can be used to analyze spatial, temporal or taxonomic trends, for example using a meta-analysis framework.