In this study, we surveyed the taxonomic diversity of airborne and surface ocean bacterial communities over 15,000 kilometers in the Atlantic and Pacific Oceans. Differences in bacterial community compositions and variability are observed between the ocean and the atmosphere. Greater resemblance was observed between the Atlantic and Pacific surface waters than their overlaying atmosphere and atmospheric samples from different locations share more common taxa than to the ocean underneath. We further provide evidence for a non-random dispersion of bacteria between the ocean and the atmosphere, indicating biodiversity constraints on dispersion. This study provides critical insights to advance our understanding of microbial dispersion in the oceanic surface water, the atmosphere, and the interchange between them, and their impact on local and global genetic composition, ecology, and biogeochemistry.