Diaminopimelic acid (DAP) is a characteristic component of peptidoglycan in Gram negative bacterial cell walls, and is an important component of organic matters in the ocean. Microbes play a vital role in promoting the recycling of marine DAP. However, neither the DAP content nor the DAP-utilizing microbes in the ocean have been investigated. Here, we measured the DAP contents in seawaters and investigated the diversity of marine DAP-utilizing microbes and their mechanism for DAP metabolism. The DAP contents are from 0.590 μM to 0.948 μM in the Western Pacific seawater from surface to 5000 m depth. DAP-utilizing bacteria of 20 families from 4 phyla were recovered from the Western Pacific seawater, and 14 strains were further isolated, which showed that Proteobacteria are the dominant group to utilize DAP. Based on genomic and transcriptional analyses combined with in vitro activity detection, DAP decarboxylase (LysA) is a key enzyme involved in DAP metabolism in the isolated Proteobacteria strains, which catalyzes the decarboxylation of DAP to form lysine. MurE and MurF are also two key enzymes for DAP metabolism, which are responsible for the incorporation of DAP into peptidoglycan for cell wall construction. Investigation in the TARA and GOS databases showed that microbes containing LysA-like sequences, which are predominantly Proteobacteria, are widely distributed in multiple habitats in the ocean, suggesting that DAP-utilizing microbes are widely spread in the ocean. This study provides the first insight into bacteria-driven DAP mineralization and recycling in the ocean.