Typical marine arthropods (crustaceans and halacarid mites), as well as species of recent terrestrial ancestry (insect larvae and mesostigmatid mites) coexist on mangrove pneumatophores. Both groups are affected by desiccation and are less abundant towards the tips of the pneumatophores. The degree of species associations within and between the two groups was investigated. The number of negative associations is higher for marine–marine, as compared to terrestrial–terrestrial and terrestrial–marine species pairs. When environmental stress (as represented by direct sunlight, and elevation on pneumatophores, both resulting in increased desiccation) is considered, associations tend to shift from negative to positive, and this is more obvious in terrestrial–terrestrial species pairs. These results are attributed to the longer co-evolutionary history of the marine species, resulting in a more precise partitioning of the microhabitats, while the relationships between terrestrial species are less stable, and more susceptible to environmental stress.