Macrolophus pygmaeus is commercially employed in the biological control of greenhouse and field vegetable pests. It is morphologically undistinguishable from the cryptic species M. melanotoma, and this interferes with the evaluation of the biological control activity of M. pygmaeus. We analysed the potential of cuticular hydrocarbon composition as a method to discriminate the two Macrolophus species. A third species, M. costalis, which is different from the other two species by having a dark spot at the tip of the scutellum, served as a control. Sex, diet and species, all had significant effects in the cuticular hydrocarbon profiles, but the variability associated to sex or diet was smaller than among species. Discriminant quadratic analysis of cuticular hydrocarbons confirmed the results of previous molecular genetic studies and showed, using cross-validation methods, that M. pygmaeus can be discriminated from M. costalis and M. melanotoma with prediction errors of 6.75% and 0%, respectively. Therefore, cuticular hydrocarbons can be used to separate M. pygmaeus from M. melanotoma reliably.