Fluctuating asymmetry (FA), defined as random deviations from perfect symmetry, has become a popular tool with which to examine the effects of stress during the development of bilaterally symmetrical organisms. Recent studies have suggested that FA in otoliths may serve as an indicator of stress in fish larvae. We examined the relationship between otolith asymmetry and temporal patterns in the occurrence of late-stage larvae to a tropical reef (i.e. replenishment) for the Caribbean lizardfish, Saurida suspicio (family Synodontidae). Late-stage larvae were collected in light traps over a period of 18 consecutive lunar months in the San Blas Archipelago, Panama. Asymmetry within otolith pairs was calculated from 24 variables: area, perimeter, longest and shortest axis of the otolith and 20 shape descriptors (Fourier harmonics). Otolith asymmetry was correlated strongly with fluctuations in lunar light trap catches. Two measured variables, otolith area and one of the 20 shape descriptors, accounted for 60% of the variability in lunar replenishment of S. suspicio. Individuals from small replenishment pulses exhibited higher levels of asymmetry compared to larvae from large pulses. When dry and wet seasons were analysed separately, otolith asymmetry explained a surprising 70 and 97% of the variation, respectively. Although the generality of these results remain to be tested among other populations and species, otolith asymmetry may be an important indicator, and potentially a predictor, of larval quality and replenishment success.