Larvae of the western rock lobster (Panulirus cygnus) that occur in the south-east Indian Ocean offshore of Western Australia have been found to be in poorer nutritional condition in anticyclonic compared with cyclonic mesoscale eddies. The reason for this is unknown, but culture-based experiments have shown that diet composition and water temperature are key determinants of phyllosoma health and survival. Whether differences in prey composition are the cause of poor phyllosoma condition in situ was tested in the present study by high-throughput sequencing of 18S rDNA amplified from the gut contents of 48 lobster larvae from two cyclonic and two anticyclonic eddies.We determined that phyllosoma prey composition did not vary significantly between anticyclonic and cyclonic eddies and that any variation was at the level of sample site (permutational multivariate analysis of variance F2,35 ¼ 5.12, P, 0.0001). We therefore reject the hypothesis that prey composition alone during the late larval phase determines larval condition. This indicates that the competing hypotheses are more likely: for example, that eddy water temperature is responsible for reducing the condition of phyllosomas directly, or indirectly by impoverishing the nutritional value of their foodweb.