Within the genus Macrolophus (Heteroptera: Miridae), the species M. costalis (Fieber), M. melanotoma (Costa) and M. pygmaeus (Rambur) are present in the Mediterranean region on a wide variety of plant species. While M. costalis can easily be separated from the other two by the black tip at the scutellum, M. pygmaeus and M. melanotoma are cryptic species, extremely similar to one another in external traits, which have resulted in misidentifications. M. pygmaeus is an efficient biological control agent, both in greenhouse and field crops. The misidentification of these cryptic species could limit the effectiveness of biological control programs. Although morphology of the left paramere of the male genitalia has been used as a character for identification of these two cryptic species, there is controversy on the reliability of this character as a taxonomic tool for these species. Using geometric morphometric techniques, which are a powerful approach in detecting slight shape variations, the left parameres from these three Macrolophus species were compared. The paramere of M. costalis was larger and had a different shape than that of M. melanotoma and M. pygmaeus; however, no differences in size or shape were found between the left paramere of M. melanotoma and that of M. pygmaeus. Therefore, our results confirm that this character is too similar and it cannot be used to discriminate between these two cryptic species.