Changes in the offshore oceanographic processes are suspected to be the cause of a recent dramatic decline in the settlement of post-larvae of the Western Australian spiny lobster (Panulirus cygnus), which has greatly reduced the productivity from the world’s second-largest spiny lobster fishery. The present study assessed whether there are differences in the nutritional condition of the larvae of P. cygnus sampled from two pairs of cyclonic eddies (CEs) and anticyclonic eddies (AEs). Morphometric and biochemical analyses were undertaken on the mid–late-stage larvae (VI, VII, VIII) sampled offshore from two pairs of adjacent counter-rotating mesoscale eddies in the Leeuwin Current off Western Australia. The results showed that larvae captured from CEs had greater average total dry mass (P<0.001) than those from AEs. Stage VIII larvae from CEs contained more protein (P<0.008) (38.5% ±5.4s.e.) and lipid (P<0.005) (67.2% ±12.1) than did those from AEs. The possible causes for these differences are uncertain but may be related to differences in water temperatures in CEs v. AEs influencing the ability of phyllosomas to accumulate nutritional reserves.