Mangroves are dynamic ecosystems due to influence of abiotic and biotic factors, but the latter are far less studied. Interactions between key invertebrate groups, trees, and soil properties, among others, determine the community structure throughout mangrove stand developing. Covariation among these factors, however, obscures their mutual relationships in shaping mangrove community assemblage patterns. In the estuary of Pacoti River (Ceará State, northeast Brazil), we compared the diversity and distribution of brachyurans and trees among several mid-littoral areas, and their relation with sediment features, to understand their relationships in community assemblage of new mangrove stands in developing. To discriminate the relation among these variables, ordination of data (PCA) and multivariate multiple correlation (PLS) were used. Data show that intertidal establishment of Brachyura was determined primarily by sediment properties, but further spatial distribution and diversity of this key faunal group, and the tree species that establishes, can influence each other. The prop roots habitat of Rhizophora mangle supports a higher brachyuran richness, since it allows the existence of multispecific crab burrow systems underground. Our results show that Rhizophora and brachyurans are key engineer organisms involved in shaping the physical and, hence, the ecological structure of newly established mangrove stands at Neotropics.