Outbreaks of the crown-of-thorns sea star (Acanthaster planci) are likely to be strongly associated with drastic changes in larval survival influenced by food availability. However, no quantitative or qualitative data are available on the distribution of A. planci larvae in the field nor on the environmental factors that influence their survivorship. Here we use a DNA barcoding approach to describe the distribution of A. planci larvae in Sekisei Lagoon, Ryukyu Archipelago, Japan after conducting three days of high-intensity sampling. High densities (53.3 individuals/m3) of A. planci larvae were found outside of Yonara Channel, which is the largest reef channel in this lagoon. Surprisingly, most (94%) of the aggregated larvae were advanced-stage brachiolaria. Considering that it takes several days to develop to this stage, this result demonstrates that A. planci larvae were floating for some time and maintaining a high-density population. However, this dense larval cloud disappeared immediately after a typhoon. No spatial correlation was found between larval density and either nutrient or chlorophyll a concentrations, suggesting that A. planci larvae do not necessarily aggregate in nutrient-rich water. These data suggest that some high-density populations of late developmental stage A. planci larvae were produced under a low phytoplankton concentration and could potentially trigger an adult outbreak. Consequently, our data suggest that adult outbreaks may not necessarily be triggered by food availability alone.