Mariculture is known to harbor antibiotic resistance genes (ARGs), which can be released into marine ecosystems via oceanic farming ponds, posing a public health concern. In this study, metagenomic sequencing was used to decipher the profiles of quinolone-resistant microbiomes and the mechanisms of quinolone resistance in sediment, seawater, and fish gill samples from five mariculture ponds. Residues of both veterinary-specific (enrofloxacin and sarafloxacin) and prohibited quinolones (ofloxacin, ciprofloxacin, pefloxacin, norfloxacin, and lomefloxacin) were detected. We identified a total of 285 subtypes of ARGs across all samples. Pathogens played a crucial role in the prevalence and distribution of these ARGs. Out of the annotated 629 bacterial species, 42 were identified as pathogenic, predominantly belonging to the Proteobacteria phylum. Notably, the Acinetobacter genus was prevalent in the gills and exhibited correlations with various ARGs. The presence of the plasmid-mediated quinolone resistance (PMQR) genes in various bacterial species and the identification of sulfonamide resistance genes across different samples indicated the potential for cross-species and cross-environment transmission of ARGs. Metagenomic binning revealed that Exiguobacterium harbored five ARGs (vanA, vanB, fexA, msr(G), mefF), while Shewanella carried six ARGs (bla