Approximately 40% of earthworm species can reproduce by parthenogenesis. This is the case for the cosmopolitan species, Aporrectodea trapezoides, although sexual forms have been described sporadically. We analyse the genotypes and microbiomes of 30 individuals from four localities where both forms appear in order to understand the evolutionary mechanisms related to parthenogenesis. In all sites, heterozygosity values were approximately 30% higher in parthenogenetic individuals. However, we detected a stronger genomic structuring due to the reproduction than to the geographical setting only in the Algerian population, underpinned by 195 loci. These loci were mapped against the annotated transcriptome of A. trapezoides using FANTASIA, finding annotations in 105 of them. This Gene Ontology (GO) terms obtained were related to gamete production, such as oocyte fate dermination and flagellated sperm mobility. We also found several other GO terms were involved in the processes mediating with other organisms including symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint and actin-dependent intracellular transport of virus towards nucleus. The transcriptome was the novo assembled using Trinity v2.11.0 . Open Reading Frames (ORFs) were inferred with TransDecoder v.5.5.0.