Abstract This study investigated the relationship between genetic and morphological evidence in a species complex of haplodiploid, near-inbred ambrosia beetles, which are also vectors of an invasive tree pathogen: Xyleborus ferrugineus, Xyleborus bispinatus, and Xyleborus impressus. The unorthodox genetic system may blur species boundaries and challenges the applicability of standard species concepts. Haplo-diploid scolytine systematics is rife with contentious species delimitation, but species limits have rarely been tested empirically. To test the congruence of morphology, genetics, and geography in species identity, we analyzed 16 morphological characters and two DNA barcodes (COI mtDNA and CAD DNA sequences) in samples from across Florida. Morphological characters used to distinguish species corresponded with phylogenetic relationships in the majority of individuals. The maximum intraspecific divergence for the COI barcoding region was up to 19%, among the largest reported for animals. The phylogenetic and morphological analyses suggest that the three species are valid, but the astonishing intraspecific genetic diversity suggests either additional cryptic species or pseudogenes.