Sexually dimorphic recombination in functional regions may arise as a consequence of sex differences in DNA double-strand breaks (DSBs) that initiate recombination and/or their downstream resolution. To investigate further, we used published male recombination initiation maps22, and find that male DSBs are significantly depleted around the TSS, with 4.4% of them overlapping a male DSB peak within 1 kb compared to an expected 5.1% (CI: 4.8–5.5%) overlap at a random position (Supplementary Fig. 15), providing independent evidence for suppressed male recombination at the promoter region of genes. Finally, we investigated recombination at CpG islands, which are known sites of transcription initiation. In females, we observe an elevation of recombination rate at these sites that is again absent in males (Supplementary Fig. 16). These different lines of evidence suggest that female meiosis is permissive of crossover activity at the site of transcription initiation whereas male meiosis suppresses recombination at these sites.