Dinitrophenylazo dyes can form 2-phenylbenzotriazoles (PBTAs) in the textile dyeing process upon the addition of chemical reducing agents. Some dinitrophenylazo dyes, as well as their respective reduced (non-chlorinated) and chlorinated PBTAs, are now found in rivers owing to wastewater from textile plants. This study aimed to investigate the genotoxicity of a new PBTA derived from C.I. Disperse Violet 93 azo dye, namely non-Cl PBTA-9. Primary DNA damage in the blood, liver, and colon cells, micronucleated cells in the bone marrow, and gene expression (NAT2, CYP1A1, TRP53, and CDKN1A) in liver cells were observed in mice, at acute oral exposure (gavage) doses of 5, 50, and 500 μg/kg body weight. The non-chlorinated PBTA-9 caused DNA damage in the blood and liver (at 500 μg/kg bw) and in colon cells (at 5, 50, and 500 μg/kg), and increased the frequency of micronucleated cells in the bone marrow (at 5 and 50 μg/kg). No histological alterations or gene expression changes were observed. In conclusion, in vivo exposure to non-chlorinated PBTA-9 induced genetic damage in various rodent tissues, corroborating results previously obtained from the Ames test. Because this compound has been detected in rivers, exposure to humans and biota is a major concern.