Marine heterotrophic prokaryotic production is commonly measured using leucine or methionine incorporation, yet how transporter composition influences amino acid uptake in marine prokaryotic communities remains unclear. Here, we analyzed global marine metagenomic and metatranscriptomic datasets to investigate the distribution and expression of leucine and methionine transporters from surface to bathypelagic waters. Leucine transporters were dominated by Alphaproteobacteria, particularly SAR11 and Rhodobacterales, whereas methionine transporters were primarily associated with Alphaproteobacteria, Gammaproteobacteria and SAR202. The methionine-to-leucine transporter ratio increased with depth in both metagenomes and metatranscriptomes, indicating enhanced methionine acquisition in the deep ocean. Distinct depth-dependent taxonomic shifts were observed, with Rhodobacterales and Gammaproteobacteria becoming increasingly important in deeper layers for methionine uptake. Notably, SAR202 exhibited elevated methionine transporter expression in the mesopelagic, supporting its role in marine sulfur cycling. These results reveal contrasting ecological strategies for leucine and methionine assimilation across marine prokaryotic communities and suggest that methionine uptake may represent an energy-saving adaptation in the deep ocean. Our findings further indicate that transporter composition may influence amino acid incorporation-based estimates of heterotrophic production, particularly in bathypelagic ecosystems.