Abstract Huanglongbing, a devastating citrus disease, is associated with ‘ Candidatus Liberibacter asiaticus’, ‘ Ca. L. africanus’ or ‘ Ca L. americanus’, bacteria transmitted by the psylloids Diaphorina citri and Trioza erytreae . Using a DNA-Seq and metabarcode sequencing integrated approach, the first catalogue of endosymbionts associated with T. erytreae from the Iberian Peninsula, South Africa and African Islands, was generated. The almost complete genome of two new bacteria, one facultative and one obligate, tentatively named Asaia-like endosymbiont of T. erytreae and Sodalis-like endosymbiont of T. erytreae, respectively, was assembled and annotated. The complete mitochondrial genomes of T. erytreae from the geographical areas studied were also assembled and phylogenetic analyses were performed, suggesting that T. erytreae populations currently present in the Iberian Peninsula and specimens analyzed from South Africa may have originated from a common ancestor. Similar results were obtained when the genetic distances between Sodalis-like endosymbiont of T. erytreae were taken into consideration, thus supporting the symbiont–host codivergence which suggests that this bacterium is approaching to an obligate status. Finally, a new genetic marker of T. erytreae, an insertion in the mitochondrial tRNA-Ser gene, was identified only in some European samples, showing for the first time the existence of two mixed subpopulations of T. erytreae . The integrated DNA-Seq and metabarcode sequencing approach used in this study, besides generating a catalogue of T. erytreae endosymbionts, provided novel data on the sequence variability of bacterial and insect mitochondrial genomes from different geographic areas, highlighting the possible original sources of currently spreading T. erytreae populations may be more complex than previously reported.