Phylogenetic analysis using DNA sequence data from two nuclear genes was undertaken to investigate phylogeographic structure within the widespread leafmining pest Liriomyza huidobrensis (Blanchard). Parsimony analysis of 171 bp from β-tubulin (including an intron) and 921 bp from elongation factor-1α confirms previous findings from mitochondrial sequence data of deep phylogeographic structure indicative of cryptic species within L. huidobrensis. We resurrect the name L. langei Frick for the North American cryptic species and restrict the name L. huidobrensis to the South and Central American cryptic species. Results from nuclear genes also confirm previous results suggesting that recent invasions of this leafminer in many areas of the world are due to the spread of L. huidobrensis from South or Central America.