Haemulidae fish, belonging to the suborder Percoidei of the order Perciformes, are important commercial marine fish species in China. Morphologically, classification controversies still exist among the genera and species of this family. To clarify such controversies, in this study, partial mitochondrial cytochrome b sequences of 66 Haemulidae species and their related families/genera were determined and analyzed. Combining this with AFLP marker information, the molecular phylogenetic relationships of Haemulidae and related species were then constructed and investigated. The phylogenetic trees were constructed based on the Cyt b gene sequences using the maximum likelihood method and based on AFLP markers using the UPGMA method. The results showed that in the Cyt b gene, 739 bp homologous sequences from 66 species were obtained, with 243 amino acids encoded; in the AFLP fingerprints, based on six primer pairs, a total of 669 clear polymorphic bands were obtained, with a polymorphic ratio of 100%. Genetic distances among Haemulidae and related families/genera (Terapontidae, Scolopsis, Hapalogenys) calculated by MEGA 7.0 revealed that the distance values between Haemulidae and Terapontidae (Cyt b: 0.191–0.275; AFLP: 1.268–1.683), Haemulidae and Hapalogenys (Cyt b: 0.180–0.297; AFLP: 1.225–1.556), and Haemulidae and Scolopsis (Cyt b: 0.208–0.290; AFLP: 1.097–1.553) were all larger than the Haemulidae intra-genera genetic distance values (Cyt b: 0.024–0.243; AFLP: 0.690–1.362), indicating their distant relationship with Haemulidae. The phylogenetic trees constructed by Cyt b genes and AFLP marker information revealed similar topologies. In the phylogenetic tree the following was found: 1) Haemulidae species were divided into two major groups, seven genera (including Pomadasys, Haemulon, and Anisotremus) were clustered into the Haemulinae group and three genera (namely, Plectorhinchus, Diagramma, and Parapristipoma) were clustered into the Plectorhynchinae group; 2) the genera Hapalogenys and Scolopsis were not clustered together with the Haemulidae group. Hapalogenys formed a separate branch and Scolopsis was clustered together with family Nemipteridae; and 3) species of family Terapontidae were not clustered with Haemulidae. Terapontidae showed a close relationship with the families Kyphosidae and Oplegnathidae. Our study supported the view that Haemulidae comprised two subfamilies, Haemulinae and Plectorhynchinae; and Terapontidae. Hapalogenys and Scolopsis may not be classified into Haemulidae. The present study revealed the phylogenetic relationships within Haemulidae and related families/genera, which provide molecular evidences for analyzing and clarifying the controversies regarding their morphological classifications.