The present study aims to evaluate the vertical distribution of intertidal benthic organisms in different periods of the year, relating them to tide, air temperature, height and wave periodicity in breakwaters off the northern Rio de Janeiro State, and to compare the zonation at two sites (Pier and Barra) with distinct hydrodynamics, due to different wave swell. Quadrats of 400 cm2 were sampled by a photoquadrat method. The upper limit of the marine organisms was higher at the Barra site (intertidal zone of 3.8 m) than at the Pier site (intertidal zone of 2.2 m). The littoral fringe assemblage did not show significant differences between sites, but a larger range of this fringe and the upper eulittoral band at Barra was quite evident. This site was mostly characterized by species of more exposed areas such as Chaetomorpha sp. and Perna perna in the upper and lower eulittoral bands, and by C. teedii and Ulva fasciata in the sublittoral fringe. A seasonal difference was identified in the air exposure degree at the Pier site, which was higher in October 2005 and February 2006. The air temperature and wave height and periodicity differed significantly among the four studied periods. The typical seasonal species were F. clenchi (July 2005 and October 2005), Gigartina domingensis (July 2005), Grateloupia sp. (October 2005) and Porphyra acanthophora (October 2005 and February 2006). The intermediate benthic band of the intertidal zone occupied a narrow zone, changing its spatial location according to the season of the year. The hypothesis of annual variation of the benthic community zonation according to the seasonal variability of tides, air temperatures and wave's height and periodicity was accepted for the intermediate band of the intertidal zone, due to the taxonomic differences and the abundance of dominant species in the four seasons. The difference in the vertical distribution of the intertidal benthic assemblages of both breakwaters highlights a distinct wave exposure condition, and reflects the breakwaters' orientation and the wave swell at each site.