Recent studies using acoustic techniques suggest that the biomass of mesopelagic fishes may be an order of magnitude higher than previously estimated from trawls. However, there is uncertainty surrounding these estimates, which are derived from shipboard echosounder measurements using necessary, but poorly constrained, assumptions. Here, an echosounder is used to measure individual target strengths at depth. These measurements are used to infer mesopelagic organism density through echo-counting. Measured target strengths are used to estimate organism density by inverting shipboard echosounder measurements. The two sampling methods agree well, but highlight the importance of accurate target strength measurements.