Species of Liriomyza Mik (Diptera: Agromyzidae) occur worldwide and are economically important leafminers. However, populations of some pest species, although very similar morphologically, show highly divergent mtDNA sequences, suggesting that nominal species are in fact complexes of cryptic species. This study focuses on two globally invasive pests, L. huidobrensis (Blanchard) and L. sativae Blanchard, already known to be highly destructive in Brazilian crops, although only a few studies on morphological and genetic divergences of them have been made. A total of 63 sequences of the mitochondrial cytochrome oxidase I (COI) and cytochrome oxidase II (COII) from Brazilian populations of L. huidobrensis and L. sativae collected from six crops (gypsophila, chrysanthemum, melon, watermelon, tomato, and onion) in Northeastern Brazil were generated to investigate their genetic structure together with available sequences from the Americas, Europe, Asia, Africa, and Australia. Genetic structure was not found to be correlated to neither host plant nor geographical locality. Liriomyza huidobrensis showed an overall low intraspecific global genetic divergence in both genes. On the other hand, high intraspecific divergences for L. sativae and its phylogenetic position confirm a divergent clade currently found only in Brazil and suggest it may be a global complex of cryptic species. Considering the possibility of cryptic species (in the latter case), we provided detailed redescriptions of these Brazilian populations for future studies and local management of these global pests. Finally, our results also revealed a new synonym herein proposed, L. strigosa Spencer as a junior synonym of L. huidobrensis.