Congenital radioulnar synostosis (RUS) is a rare skeletal disorder that is characterized by fusion of the radius and ulna. As the etiology of RUS is largely unknown, its treatment options are currently limited. A de novo missense mutation in the zinc finger matrin-type 2 (ZMAT2) gene was newly identified in a 5-year-old boy with RUS using whole-exome sequencing. Herein, we sought to further explore the function of zmat2 in zebrafish. Whole-mount in situ hybridization revealed site-specific expression of zzmat2 in the pectoral fins (equivalent to human upper limbs) and craniofacial regions, while immunohistochemistry showed the expression of zZmat2 in the pectoral fins and heart region. Gene knockdown produced defects in the pectoral fins and dorso-ventral patterning. zzmat2 knockdown also caused embryo dorsalization, a phenotype consistent with reduced/insufficient bone morphogenetic protein (BMP) signaling. These abnormalities were partially rescued by zbmp2b RNA overexpression and fully rescued by simultaneous overexpression of wild-type zzmat2. Importantly, the overexpression of mutant zzmat2 corresponding to the newly-identified mutation did not fully rescue the dorso-ventral patterning defects. The above findings indicate that ZMAT2 regulates skeletal development via the BMP signaling pathway, and its mutation may lead to a loss or reduction in biological activity. Thus, the newly identified ZMAT2 mutation potentially plays a causal role in RUS through deregulation of BMP signaling.