Currently, although enrofloxacin (EF) as a widely used veterinary medicine has begun to apply to treating fish bacterial infections, the researches on the effects of EF on their main drug metabolic enzymes are limited. To investigate the effects of EF on fish cytochromes P450 (CYPs) 1A and 3A, the enzymatic activities and expressions (mRNA and protein) of crucian carp CYP1A and CYP3A after EF administration were examined. For CYP1A, in the in vivo experiments, EF exhibited potent inhibition on the CYP1A-related ethoxyresorufin-O-deethylase (EROD) activity, as well as CYP1A expressions at both protein and mRNA levels, at 24 h after administration with different EF dosages (3, 10, 30, and 60 mg/kg); Furthermore, CYP1A enzymatic activity and expressions at both protein and mRNA levels decreased more with increasing EF dosages. Additionally, the in vitro experimental results showed that, after incubated with microsomes, EF did not change the EROD activity through interacting directly with CYP1A. For CYP3A, the in vitro and in vivo experimental results demonstrated that EF could inhibit the CYP3A-related erythromycin N-demethylase activity in a time- and dose-dependent manner, while it did not suppress CYP3A expressions at both protein and mRNA levels after administration with EF for a short period (no more than 24 h); however, after injection with EF at a high dose (10 mg/kg) for a long period, the CYP3A protein and mRNA reached their lowest levels at 96 and 48 h, respectively. These results indicate that EF can suppress CYP1A expressions in a dose-dependent manner, thereby inhibiting further its catalytic activity; meanwhile, both the interactions of EF with CYP3A and the expressions decrease (protein and mRNA) caused by EF contribute to the CYP3A inhibition.