Host resistance evolution to natural enemies depends on genetic variation, symbiont associations, and trade-offs with host´s fitness traits. We selected isofemale lineages of Myzus persicae to investigate biological traits and molecular markers associated with aphid defensive responses to the parasitic wasp Diaeretiella rapae. The parasitization of M. persicae lineages by D. rapae ranged from 43 to 76%. Rickettsia was the predominant secondary symbiont. Six lineages were selected according to D. rapae parasitization rate (LP=low parasitization; HP=high parasitization) and Rickettsia association. Life history traits differed among M. persicae lineages. However, the association of adaptive costs with reduced susceptibility to D. rapae parasitization was not consistently observed. Rickettsia infection did not explain the enhanced aphid defense, but it did increase aphid fecundity. Comparative small structural variants analyses of M. persicae lineages indicated that approximately 6% of SNPs and 49% of InDels were unique to each aphid lineage or shared among LP or HP lineages. Only 1.7% of SNPs and 0.91% of InDels influenced genes involved with aphid immune response. Further exploration of non-coding variants and additional omics-related approaches are needed to fully characterize the mechanisms behind the differential parasitization success of M. persicae lineages by D. rapae.