Multi-specific seagrass meadow assemblages dominate most tropical intertidal regions but the relative role of environmental stress in determining distribution patterns is still uncertain. Here we combine observational and experimental approaches to examine aerial exposure as a factor driving species occurrence patterns in intertidal meadows of the Andaman archipelago, where up to 6 seagrass species co-occur. In the studied meadow, patterns of exposure did not map onto distance from the coast, instead creating a patchy matrix of exposure, based on fine-scale bathymetric differences. Distributional surveys showed that seagrass species were similarly patchy, often tracking the degree of aerial exposure during low tide. While some species (Halophila ovalis, Halophila minor, and Thalassia hemprichii) frequently occurred in submerged or subtidal areas and were rarely found in completely exposed areas, other species (Cymodocea rotundata, Halophila beccarii, and Halodule uninervis) also occupied areas that were subject to partial or complete aerial exposure during low tide. To confirm this pattern, we used field-based transplant experiments, employing a natural gradient of tidal exposure to subject six seagrass species to different desiccation exposure times. After a month, H. beccarii and H. uninervis transplants survived in areas that sustained more than 3 h of aerial tidal exposure without significant mortality, compared with other species (H. ovalis, H. minor, T. hemprichii, C. rotundata) that showed dramatic shoot mortality at the same exposure regimes. For all species, 4 h represented the upper limit of exposure, in both experimental and distributional studies. However, despite their wider tolerance of exposure to air, H. beccarii and H. uninervis did not dominate the entire meadow. This could be a result either of their poor tolerance to other environmental factors or their lower competitive abilities among other mechanisms. This suggests that in tropical multi-specific meadows, strong environmental filters could override clear intertidal zonation to create patchy matrices based on species tolerances.