The study aims to analyze diurnal migration of zooplankton in Ambon Bay. Data sampling method which is conducted stationary utilizes pontoon mooring as floating platform for acoustic data sampling. Based on the analysis, diurnal migration of zooplankton occurs at noon, zooplankton swims in water surface to epipelagic zone (0-20 m) with value of scattering volume value -90.13 dB to -100.30 dB; it indicates sparse and scattered aggregation (N=128). At night, scattering volume of -90.01 dB to -100.30 dB indicates dense and concentrated aggregation (N=75). Scattering volume is numerical expression of zooplankton density. Chlorophyll a concentration in depth of 0-10 meter having the highest value of 5.16 ppb highly affects the existence of zooplankton. It functions for food availability of pelagic fish as its carnivore.