High- and multi-frequency acoustic systems can measure a zooplankton patch successively and estimate the spatial distribution and abundance of zooplankton according to size using a multi-frequency inversion (MFI) method. This study measured zooplankton distribution to a depth of 150m using a multi-frequency acoustic system (TAPS-6), installed on a CTD system with a fluorometer and analyzed it using the MFI method. Simultaneously, zooplankton samples were collected by north pacific standard (NORPAC) net to confirm the species composition. The results showed that the combined method is valuable for estimating the zooplankton profile in detail and investigating the relationship between the zooplankton and phytoplankton profiles.