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Antagonistic co-evolution between pathogens and their hosts can drive rapid adaptive changes in both partners. We aim to understand the underlying mechanisms driving rapid adaptation in two closely related fungal plant pathogens <i>Zymoseptoria tritici</i> (wheat pathogen) and <i>Z. ardabiliae</i> (wild grass pathogen). We previously showed a significantly higher effective population size in <i>Z. tritici</i> in spite of strong directional selection pressure imposed to the pathogen in the wheat field. Also we showed a strong impact of natural selection on genome evolution in <i>Z. tritici</i>. A high efficacy of selection may be mediated by recombination. We applied a population genomics approach to infer genome-wide recombination maps in <i>Z. tritici</i> and <i>Z. ardabiliae</i>. Comparing mean recombination rates of coding and non-coding sequences, we find significantly higher recombination rates in coding sequences implying a central role of recombination in gene evolution. Some genes are located in recombination hotspots further supporting a central role of recombination in gene evolution. In both species recombination rate varies across chromosomes. We correlated recombination maps in the syntenic genomes of <i>Z. tritici</i> and <i>Z. ardabiliae</i>. Some regions have conserved patterns of recombination while others show highly different patterns. We conclude that patterns of recombination rate evolve in <i>Zymoseptoria</i> allowing orthologous genes to evolve at highly different rates in <i>Z. tritici</i> and <i>Z. ardabiliae</i>.