The Amazon basin is considered the largest drainage system in the world at approximately 700,000 km, and it is composed of approximately 7,000 tributaries. Throughout this large area, very different environments exist, including different water types. Based on physical and chemical factors, a classification system of the Amazonian waters has been suggested. This system distinguishes between white, clear and black waters. White water presents a high concentration of minerals, a neutral pH (6.5 to 7.0) and high conductivity. Clear water presents variable pH (4.5 to 7.0) and relatively low conductivity. Finally, black water presents a high concentration of humic acids, which result in dark hues and acidic pH levels. Black water also has a low concentration of minerals and an absence of calcium and magnesium ions. In spite of the environmental variations found among the types of Amazonian waters, some fish species, such as Colossoma macropomum, may be found in all of these environments. This species occupies a prominent position in Brazilian fishery and aquaculture, and it is known for its features such as the flavor of the meat, their large body size, and their easy adaptation to captivity. In general, some factors such as disease, pollution, temperature change and other environmental adversities that expose an organism to stress lead to the mobilization of transposable elements (TEs). Transposable elements (TEs) are DNA sequences that have the intrinsic ability to move and replicate within genomes. They share characteristics such as promotion of duplication, polymorphism of insertion sites, and copy number variability within and between species. TEs can be classified according to their transition intermediates: RNA (Class I or retrotransposons) or DNA (Class II or DNA transposons). TE mobilization is subject to a complex set of regulatory mechanisms that involve protein encoded not only by the transposon, but also by the transposon hosts. In recent decades, several studies have revealed the extent of the participation of the environment in the expression and/or activation of retrotransposons in studies on various organisms such as plants, insects of the genus Drosophila, shrimp, fish and mice. Fish have a particularly large number of active retrotransposons, and many are unique to this group. Thus, fish are an important model for studies on the evolution, dynamics, and especially the influences of the environment on retrotransposon expression. Even so, studies involving the expression of retrotransposons in fish are scarce.