This paper presents an overview of the composition and abundance of pelagic fish communities collected during the 43rd cruise of the R/V ′Akademik Sergey Vavilov' on the transect in the central Atlantic, from the Azores to the Equator, in autumn 2016. Samples were taken only at night with a Samyshev-Aseev modified Isaacs-Kidd non-closing midwater pelagic trawl (SAMT) at 18 stations from two depth of 0–200 and 0–700 m. The study recorded 112 species of juvenile and adult mesopelagic fishes belonging to 20 families at the sampled stations. The statistical analysis indicated notable disparities in the fish communities that were caught at depths of 0–200 and 0–700 m. Our study suggests that there are notable differences in pelagic fish associations between the North Atlantic anticyclonic gyre zone and the equatorial jets region, at both depths analyzed. These differences are most likely the result of variations in hydro-physical and other environmental parameters. It has been observed that deep-sea fish communities in the equatorial and central North Atlantic are capable of inhabiting at the same time multiple habitats that exhibit varying physical and chemical structures of water masses. This phenomenon highlights the remarkable ecological adaptability of the species that make up mesopelagic deep-sea communities, as well as their wide geographical distribution. The higher abundance and diversity of mesopelagic fishes observed at stations located above the Mid-Atlantic Ridge may be due to a general decrease in depth over the ridge compared to the surrounding regions and/or local circulations occurring over its crests. Thus, the tops and slopes of seamounts may become unique concentrations of mesopelagic fishes for a limited time due to their topography.