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In asexual animals, female meiosis is modified to produce diploid oocytes. Associated with recombination, this is expected to lead to a rapid loss of heterozygosity, with adverse effects on fitness. Many asexuals, however, have a heterozygous genome, the underlying mechanisms being most often unknown. Cytological and population genomic analyses in the nematodeMesorhabditis belarirevealed another case of recombining asexual being highly heterozygous genome-wide. We demonstrated that heterozygosity is maintained because the recombinant chromatids of each chromosome pair co-segregate during the unique meiotic division. A theoretical model confirmed that this segregation bias is necessary to account for the observed pattern and likely to evolve under a wide range of conditions. Our study uncovers a new type of cell division involving Directed Chromatid Assortment.One sentence summaryGenome wide heterozygosity in the asexual nematodeMesorhabditis belariis achieved by directed assortment of recombinant chromatids during female meiosis