Microbiome insect research has grown rapidly over the last years thanks to advances in next-generation sequencing. The bacterial microbiome inhabiting insects often involves mutualistic associations between the insect hosts and maternally transmitted symbiotic bacteria. Among insect groups, aphids are the most studied regarding insect symbiosis, but with a strong bias toward a few well studied species. Increased resistance to parasitic wasps, entomopathogenic fungi and tolerance to thermal stresses are the most common facultative endosymbiont-mediated effects in aphid biology. Here, we studied the microbiome of the woolly apple aphid Eriosoma lanigerum, a severe pest of apple orchards, which has been poorly studied concerning facultative symbionts. Our 16S rRNA gene Illumina sequencing-based taxonomic assignment, showed a high representation of reads assigned (99% similarity) to a recently recognized bacterial taxon, not previously described in aphids, identified as Symbiopectobacterium purcellii. This bacterial endosymbiont has been recognized as a new clade of Enterobacteriaceae, vertically transmitted and mutualistic in various invertebrate hosts, including one nematode species and four insect species from the order Hemiptera. This finding emphasizes the need to extend the study of symbionts from entire microbiomes of insect hosts, to understand the diversity of endosymbionts across host species and their role in insect ecology.