Metabarcoding is revolutionising the analysis of biodiversity in marine ecosystems as it provides a means of detecting and identifying cryptic life-stages. Many marine species, including echinoderms, possess an elusive pelagic larval stage that underpins the abundance and distribution of adult populations. Insight into the dynamics of early life-stages could be invaluable as fluctuations in the adult population density of echinoderms, like the crown-of-thorns seastar (CoTS), can significantly affect local ecosystems. In this study, we aimed to validate the use of metabarcoding for the detection of echinoderm larvae in field samples, and gain insights into the life-history of this phylum. We analysed plankton samples collected at Moore Reef between 2015-2020, and along a latitudinal gradient from Lizard Island to Fore and Aft Reef on the Great Barrier Reef. Echinoderm larvae were found to exhibit seasonal changes in community composition and richness at Moore Reef. In contrast, community composition and richness were not correlated with latitudinal gradient or particular reefs in our dataset. Our findings suggest that metabarcoding can be used to better understand the life history of pelagic larvae, and we were able to confirm its utility for the surveillance of CoTS larvae, which could prove useful to future management efforts.