The MER3 gene is identified as a novel meiosis‐specific gene, whose transcript is spliced in an MRE2/MER1‐dependent manner. The predicted Mer3 protein contains the seven motifs characteristic of the DExH‐box type of helicases as well as a putative zinc finger. Double strand breaks (DSBs), the initial changes of DNA in meiotic recombination, do not disappear completely and are hyperresected late in mer3 meiosis, indicating that MER3 is required for the transition of DSBs to later intermediates. A mer3 mutation reduces crossover frequencies, and the remaining crossovers show random distribution along a chromosome, resulting in a high incidence of non‐disjunction of homologous chromosomes at the first meiotic division. MER3 appears to be very important for both the DSB transition and crossover control.