We examined the abundances of two species of benthic foraminifera that host algal endosymbionts (SBF) in two sedimentary reefal areas (Pirangi and Maracajaú) of Rio Grande do Norte (RN, Brazil). The original dataset is based on 95 samples collected in winter in 2013 and 2014 by divers or grab samplers, and is compared to other known Brazilian reefs. The tests of Amphistegina gibbosa were conspicuous in sediments associated with coral and coral-rubble substrata, whereas tests of Amphisorus hemprichii were best represented in sediments associated with seagrass. Our studies also have revealed that populations of these species are depauperate near tourism sites in Pirangi, as the area is affected by trampling from tourist activities. In the Maracajaú area, these populations are healthier, except at sites severely affected by tourism. Differences in microhabitats of the two taxa are likely to be associated with the degree of anthropogenic influence on the inner shelf at Pirangi compared to the offshore Maracajaú area.