During meiosis, homologous reciprocal recombination events or crossing-over determine the genetic map and are known not to be randomly distributed in the genome. Recent studies in yeasts and mammals reveal some key features of the molecular mechanism involved in this distribution. Through different molecular processes, specific histone post-translational modifications are induced at specific genomic sites, called hotspots, where initiation of meiotic recombination takes place. These sites are some transcription promoters in S. cerevisiae or binding sites for transcription factors in S. pombe, where chromatin modifiers are recruited. In mammals, the sites are DNA sequences recognized by the PRDM9 protein which has the ability both to bind DNA and to induce the trimethylation of the lysine 4 of histone H3. The properties of the chromatin at these sites, and potentially the binding of additional factors, allow the recruitment of proteins involved in the formation of DNA double strand breaks that initiate meiotic recombination.