This　study　investigated　the　bacterial　communities,　metabolic　functions,　antibiotic　resistance　genes　(ARGs)　and　metal　resistance　genes　(MRGs)　in　two　alternating　anaerobic/aerobic　biological　filters　(A/O-BFs)　treating　saline　seafood　wastewater　(SSW).　Firmicutes　was　the　most　abundant　phylum　in　both　systems,　and　halophilic　and　alkaliphilic　bacteria　were　largely　enriched.　15　potential　pathogens　were　obtained.　Metabolism　was　the　predominant　bacterial　function.　49　ARGs　and　7　MRGs　were　detected,　and　the　total　abundance　of　ARGs　increased　while　that　of　MRGs　decreased.　Clear　shifts　in　bacterial　structure　and　function,　ARGs　and　MRGs　were　observed　in　both　systems　and　at　different　heights.　Co-occurrence　of　ARGs　and　MRGs　and　their　hosts　were　identified.　ARGs　and　MRGs　mainly　negatively　correlated　with　bacterial　functions,　which　were　also　the　important　contributors　to　shifts　in　bacterial　communities　and　functions.　This　study　highlights　the　importance　of　investigating　ARGs　and　MRGs　in　SSW　treatment　systems　and　their　complex　interactions　with　bacterial　communities　and　functions.