The first comprehensive cladistic analysis of Miridae, the plant bugs, based on ~3000 base pairs of mitochondrial (COI, 16S) and nuclear (18S, 28SD3) genes, is presented. For 105 taxa (101 Mirid species in 7 subfamilies and 11 tribes, and 4 outgroups) in 7 subfamilies and 11 tribes of Miridae, the combined dataset was analyzed using ML (maximum likelihood), BC (bayesian criteria) and MP (maximum parsimony). Clades recovered in all analyses, comprise 6 main groups: Cimicomorpha and Miridae; Phylinae; Mirinae (Eurystylus + Polymerus + Proboscidocoris + Taylorilygus + Stenodemini); Orthotylinae; Mirini (Adelphocoris group except “Apolygus complex”); Apolygus complex; Deraecorinae; Bryocorinae + Isometopinae + Cylapinae. Our results indicate 1) the monophyletic relationships of two subfamilies Phylinae and Deraeocorinae within the family Miridae; 2) the paraphyly of subfamily Mirinae. Phylogenetic relationships at the tribal or subfamily level are provided in comparison with the prior studies based on morphological data.