Benthic foraminiferal assemblages can indicate the ecological status of coral-reef ecosystems. Their functional groups have been used to calculate the previously published FORAM Index (FI), which is based on total counts (living and dead) to indicate whether an environment is suitable to support prolific calcification by organisms that are dependent upon algal endosymbionts. Sediment was sampled from the Archipelago of Fernando de Noronha and the Abrolhos Archipelago and Parcel, which harbor important coral reef communities off the NE and E coasts of Brazil. Quantifying live specimens and taphonomic features of Amphistegina spp., along with the FI in 2005 and monitoring of the percentage of coral cover from 2002–2009, provided an assessment of coral reef health, which was mapped for both areas. Results indicated that FI was good (>4) in half of the sampled stations, but no living Amphistegina was found in the Abrolhos Archipelago and Parcel, possibly indicating recently unfavorable conditions there. These findings suggest that palimpsest sediment can disguise FI so that, in some cases, the index fails to correlate with coral cover. A more realistic approach can be obtained by using the living counts of Amphistegina and their taphonomy to augment the ecological results from the FI.