Small proteins (SPs, ≤50 amino acids) are usually ignored by automated bioinformatic algorithms and difficult to be detected by traditional protein purification. In this study, 193,281 prokaryotic SP clusters were generated using 433,311 small open reading frames (sORFs) predicted in assemblies of 71 full-ocean-depth marine water metagenomes from the western pacific. Further filtration with at least 5 copies per million reads resulted in 75,581 prevalent SP clusters, among which 4,307 clusters have coding capacity as predicted by RNAcode. For these RNAcode-filtered SP (RfSP) clusters hosted largely by Proteobacteria, Thaumarchaeota and Marinimicrobia, 29.16% of them show homology () in all prokaryotic genomes. About 2% of the RfSP clusters were estimated as potential antimicrobial peptides and were distributed across all depth zones. Transcription of 7.96% of the RfSP clusters was verified in 12 deep-sea metatranscriptomes, and translation of 34 prevalent SP clusters was detected in 14 metaproteomes. The transcribed RfSP clusters are involved in processes such as DNA stability under stress condition, betaine transport and cell division regulation for a rapid response to varying deep-sea environments. This study uncovers a vast reservoir of SPs with pivotal functions in potential antibiotic activities, hyperoxide detoxification and pressure resistance for fitness of marine prokaryotes in deep ocean.