The flower bugs (Heteroptera: Anthocoridae) is usually known as biological control agents against various kinds of agricultural pests such as aphids, mites, thrips and so on. Since the classification of the family Anthocoridae has been controversial, the molecular phylogenetic study was conducted with 44 species including 6 outgroup taxa. Three genes, a total of 3277 bp of sequence data (nuclear 18S rDNA: 2022bp, 28S rDNA: 755bp, and mitochondrial 16S rDNA: 498bp), were analyzed using ML (maximum likelihood) and Bayesian methods, excluding MP (maximum parsimony) as the incongruence length difference (ILD) test has very low (0.001) P-values on all partition tests. Our results support the rank and monophyly of the family Lasiochilidae which was exclusively separated from the main clade of Anthocoridae proposed by Schuh and Stys (1991), and indicate the monophyletic relationships among tribes and genera within the family Anthocoridae. According to our results, the genus Amphiareus should be out of the tribe Dufourini and treated as the tribe level and The three genera, Blaptostethus, Scoloposcelis and Xylocoris should be placed to the family Lyctocoridae. We also propose the evolutionary theory of Anthocoridae based on their habitats, hunting behavior and the molecular phylogenetic results.