To understand and manage marine ecosystems for conservation, particle-tracking simulation based on a realistic ocean model is one of the most basic and essential scientific numerical techniques for a multidisciplinary approach. In Japanese waters, this technique was first used under somewhat simplified conditions in the 1980s, and then it continued to be developed, with the number of studies using this technique increasing drastically after the mid-2000s. At that time, mesoscale eddy-resolving ocean forecast systems moved into operational phase, and since then, those reanalysis or analysis products have been publicly shared among scientists. This article provides an overview of the history and current status of particle-tracking simulation for marine biology around Japan (e.g., target species, ocean models utilized, configurations and timescales of particle-tracking models, and related biological data) and summarizes the scientific resources to be maintained and some issues to be resolved in the next future step.