Abstract The effect of inbreeding on haplo-diploid organisms has been regarded as very low, because deleterious recessive genes on hemizygous (haploid) males were immediately purged generation by generation. However, we determined such recessive genes to decrease female fecundity in a population of Schizotetranychus miscanthi Saito which is known in the Acari as a subsocial species with haplo-diploidy. In mother–son inbreeding experiments, there was no depression in egg hatchability nor in the larval survival of progeny over four generations. There was, on the other hand, significant inbreeding depression in the fecundity with increasing f-value. Crosses between two lineages, one having deleterious effects on the fecundity and the other having no such effects, established during the inbreeding, revealed heterosis, and backcrosses showed that the depression was caused by deleterious recessive(s). These results strongly suggest the existence of some deleterious genes governing only the traits of adult females in wild populations of haplo-diploid organisms.