Facultative bacterial endosymbionts are prevalent in aphid pest species and key organisms for the rapid adaptation to changing environment conditions under agricultural management. Facultative endosymbiont interactions allow beneficial phenotypes of insect hosts, providing resistance against natural enemies, fungal infections as well as enhanced resistance to thermal conditions, among others. These interactions have been highlighted as important modulators in the evolution of aphid defenses, being a key aspect for the invasive potential of aphids as pests. In this study, we have examined the bacterial community diversity associated to the pea aphid Acyrthosiphon pisum on alfalfa (Medicago sativa L.) crops in Central Chile by determining the presence and abundance of the seven most common facultative endosymbionts reported for aphid species, including: Hamiltonella defensa, Regiella insecticola, Serratia symbiotica, Spiroplasma sp., Rickettsia sp., Rickettsiella viridis and Fukatsuia symbiotica (or pea aphid X-type symbiont’ PAXS), using a PCR-based approach across species-specific primers, in 16 alfalfa fields during the Chilean spring in the Maule Region. We reported six of the seven endosymbiont species studied, observing a high frequency of infected aphids being the endosymbiont H. defensa, the most predominant among the aphid populations in the different alfalfa fields studied. As H. defensa has been extensively studied in its defensive role to parasitoids, we discuss implications for biological control of this aphid pests. We also discuss the absence of a relevant defensive endosymbiont such as F. symbiotica in the Chilean pea aphid populations and potential implications for the success of the pea aphid biological control program.