The purpose of this study was to determine the diversity, morphometric characteristics, and species relationships of mullet species found in the estuaries of Yogyakarta Special Territory. Thus, 384 samples were collected from the Bogowonto, Serang, Progo, and Opak estuaries. The fish collected were identified based on their morphological characteristics and grouped by species. Then, the sample was measured for its total length, meristic, and morphometric characteristic. Data were analyzed using discriminant analysis, Duncan analysis, canonical analysis, and cluster analysis. The results showed six mullet species in the estuaries of Yogyakarta Special Territory, namely Chelon macrolepis, Chelon melinopterus, Chelon subviridis, Moolgarda engeli, Mugil cephalus, and Valamugil buchanani. The main difference between each species was shown by the number of lateral linear scales and the inner truss line on the side and the tail. The morphometric variation between the species of mullet ranged from 33.3 to 71.4%. Moolgarda engeli and C. melinopterus had the closest relationship, and both species were closely related to C. macrolepis. The phylogenetic relationship among species was slightly different compared to the morphometric character of their genetic characters. Morphometric variances may be seen in a variety of morphological features, including interorbital and interventral distances, as well as the distance between the cranial bones, dorsal and pelvic fins, and anal fin. The caudal peduncle height varies as well.