Micronekton organisms are a central component of the trophic organization in the pelagic ecosystem, being prey to top predators and participating in the export of carbon from the surface to the deep layers. Despite their importance, the abundancedeep sea estimates and species distribution of micronekton remain largely uncertain. This study aimed to compare and assess two sampling methods classically used for the estimation of micronekton abundance in mesopelagic acoustic scattering layers: scientific echosounder and trawl sampling. Measurements of 38 and 70 kHz hull-mounted echosounders were examined with biological trawl samples from 8 surveys in the South-West tropical Pacific. A model of acoustic observation was built from the trawl sampling species composition and forward scattering models. Predicted and observed acoustic responses are compared to assess the variability and the difference between the acoustic and trawl sampling methods in various scattering layers, for day and night periods. The difference between methods decreased with depth and with increasing abundance of fish with swimbladders caught in trawls. Notably, this difference was found to be minimal in the nocturnal deep scattering layer (mesopelagic zone, depth>200 m). This study emphasizes potential lower estimates of organisms’ abundance by trawling and a bias towards mesopelagic fish. Understanding the differences between methods and their variability within different scattering layers is essential for studying micronekton and improving the precision of biomass estimates.