This study addressed the usefulness and reliability of using a new plankton image analyzer, FlowCAM, for rapid analysis of copepod feeding by comparison with the conventional microscopic analysis. We carried out bottle incubation experiments with two copepod species in the Oyashio region and analyzed the prey abundance prior to and after the incubation with a FlowCAM. From the volume-specific fluorescence intensity of particles, the FlowCAM successfully distinguished between zooplankton and phytoplankton and allowed an adequate evaluation of the copepod feeding on zooplankton and phytoplankton. The analysis time for one plankton sample was about 10 min, which was less than one-tenth of the time required for microscopic enumeration. The FlowCAM is considered to be an efficient tool for rapid analysis of copepod feeding particularly in studies of omnivory.