Medicinal plants provide a cheaper and sustainable alternative to chemotherapy in aquaculture; however, its misuse could be potentially toxic to both aquatic animals and humans. This study aimed to evaluate the potential cytogenetic and biochemical effects of thyme and rosemary powder supplemented diets on the Nile tilapia juvenile. Fish (26±1.5 g) were distributed into 5 groups and fed a non-supplemented diet (control), supplemented diets with thyme at a concentration of 1% and 1.5%, and diets supplemented with rosemary at a concentration of 0.5% and 1% for 6 weeks. Cytogenetical assessment (chromosome aberrations, micronucleated erythrocytes, and DNA fragmentation) was performed after 2, 4, and 6 weeks of feeding. In addition, hepatic enzymes (aspartate aminotransferase, alkaline phosphatase, and alanine aminotransferase), renal indicators (urea and creatinine), and muscle damage biomarkers (creatine phosphokinase, [CPK] and lactate dehydrogenase, [LDH]) were analyzed after 2 and 6 weeks feeding. The clinically examined fish in the group fed with 1% rosemary showed restlessness and lethargy throughout the experiment. Postmortem examination of moribund fish revealed body darkness with excessive mucus secretion and paled liver with red patches. In addition, this group showed a mortality rate reached 18.66%. Dietary supplementation of 1.5% thyme and 1% rosemary for 6 weeks of feeding exhibited a little bit of cytogenetic effect on peripheral blood, head kidney, and liver tissue, as the recorded types of aberrations were not severe. Fish receiving 1% rosemary for 6 weeks showed significant increases in the activity of hepatic enzymes, CPK and LDH activities, as well as creatinine levels, compared to the control and other treated groups. The results of this study demonstrate that, although thyme and rosemary have beneficial effects as medicinal herbs, they may pose cytogenetic threats to cells of the Nile tilapia at an early life stage. Thyme at a dose of 1% was proven to be safe for the juvenile Nile tilapia.