A series of inbreeding crosses, recurrent backcrosses and successive sibling crosses were completed up to the sixth generation in the plant pathogen Phytophthora capsici, generating a total of 692 oospore-derived isolates. All of the crosses stemmed from an initial mating between two wild-type P. capsici isolates. The heterozygosity level, as measured through the inheritance of 20 amplified fragment length polymorphism (AFLP) markers, decreased incrementally with continued inbreeding and was reduced by ~60–75% by the second consecutive sibling cross. Of the eight crosses analysed, all but one cross produced a proportion of oospore-derived progeny that were identical to one or other parent, indicating that apomixis can play a role in P. capsici intraspecific crosses. There was no evidence of isolates emerging through selfing or generation of homothallic isolates. Overall, these results indicate that back and sibling crosses are possible and that the large reservoirs of naturally occurring genetic variation in P. capsici may be useful for developing inbred lines to characterize complex genetic traits in Phytophthora.