Termites are among the most important groups to maintain tropical forests but despite their importance they are poorly studied. Termites were sampled in the trunks left over from the flood period in the Balbina Hydroelectric plant (UHB). The trunks are in the water and just partially submersed without contact with the mainland. We compared the species composition with the surrounding terra firme forest. This is the first list of species provided for this area from a standardized sampling and we provide some insights into how these degraded areas can be important to study species distribution and have potential for the discovery of new species of termites. We found that the change in the environment can drastically change the species composition and some rare species in the natural landscape can be more easily detectable in these areas.