Whereas endosymbiont-induced incompatibility is known to occur in various arthropod taxa, such as spider mites, insects and isopods, it has been rarely reported in plant-inhabiting predatory mites (Acari: Phytoseiidae). Recent cross-breeding studies with the phytoseiid mite Neoseiulus paspalivorus De Leon revealed a complete post-mating reproductive isolation between specimens collected from three geographic origins-Northeast Brazil (South America), Benin and Ghana (West Africa)-even though they are morphologically similar. We carried out a study to assess to what extent these populations exhibit genetic differences and whether endosymbionts are involved in the incompatibility. First, we used the mitochondrial cytochrome oxidase I (COI) gene to assess genetic diversity among the three populations. Second, we used a PCR-based method to check for the presence of Wolbachia and/or Cardinium in these populations, and we determined their phylogenetic relationships using specific primers for Wolbachia and Cardinium 16S rDNA genes. Third, we also conducted a test using an antibiotic (tetracycline) in an attempt to eliminate the symbionts and evaluate their effects on the reproductive compatibility of their host. Based on the DNA sequences of their COI genes, specimens of the three populations appear to be genetically similar. However, the 16S rDNA gene sequences of their associated endosymbionts differed among the three populations: the Benin and Brazil populations harbour different strains of Wolbachia symbionts, whereas the Ghana population harbours Cardinium symbionts. In response to antibiotic treatment females of each of the three populations became incompatible with untreated males of their own population, similar to that observed in crossings between females from one geographic population and males from another. Compatibility was restored in crosses involving uninfected Brazil females and uninfected Benin males, whereas the reciprocal crosses remained incompatible. Cardinium symbionts seem to be essential for oviposition in the Ghana population. It is concluded that their associated bacterial symbionts are the cause of the post-mating reproductive isolation previously observed among the three geographic populations. This insight is relevant to biological control of coconut mites for which N. paspalivorus is an effective predator, because introducing one geographic strain into the population of another (e.g. in field releases or mass cultures) may cause population growth depression.