Abstract Recombination between direct repeats has been studied in Penicillium chrysogenum using strain TD7-88 (lys pyr+), which contains two inactive copies of the lys2 gene separated by 4.5kb of DNA (including the pyrG gene) in its genome. Gene conversion leading to products with the lys+ pyr+ phenotype was observed at a frequency of 1 in 3.2103 viable spores. Two types of deletion events giving rise to lys+ pyr and lys pyr phenotypes were obtained with different frequencies. Southern analysis revealed that gene conversion occurs mainly as a result of crossing over events that remove the BamHI frameshift mutation present in one of the repeats. In lys pyr recombinants, the deletion events do not affect the frameshift mutation in the BamHI site, while lys+ pyr recombinants showed repair of the BamHI frameshift mutation and the genotype of the parental non-disrupted strain was restored. In summary, deletion events in P. chrysogenum tend to favor the restoration of the phenotype and genotype characteristic of the parental non-disrupted strain.