This study investigated the influence of physical and chemical conditions and biotic factors on the distribution and diversity of meiofauna in intertidal zone along a geographical gradient. At 11 sites along the Italian coast, we studied the concurring role of environmental variables, trophic resources and the presence of habitat-forming species (macroalgae vs. mussels) in controlling the meiofaunal communities. The increase of water temperature combined with local thermal conditions was associated with a decrease in nematodes and copepods, with a consequent decrease in meiofaunal abundance towards the south. However, the increase in salinity, as geographical gradient decreases, and local thermal conditions favoured the settlement of a greater number of taxa, influencing communities' composition. The presence of macroalgae or mussels differently influenced the community structure of meiofauna on intertidal substrates and their response to environmental factors. From our results, the presence of macroalgae coverage appeared to reduce the impact of thermal stress on meiofauna and was associated with higher levels of meiofaunal diversity with respect to mussels. This work highlighted the importance of considering the interplay among biotic and abiotic factors, resulting in local combinations of environmental conditions, in order to understand the pattern of diversity and distributions of marine organisms.