Fine-scale spatial and temporal variation in the genetic composition of benthic recruits, known as chaotic genetic patchiness, is often observed in marine and estuarine species with planktonic larvae. Several explanations have been proposed for chaotic genetic patchiness, including sweepstakes reproductive success, variability in larval source, and natural selection. In a survey of the green shore crab Hemigrapsus oregonensis in Bodega Bay, California, USA, allele frequencies at a mitochondrial single nucleotide polymorphism were found to differ significantly among samples of first-stage zoeae and between zoeae and adults. Sweepstakes reproductive success is unlikely to be responsible because the fecundity of this species is too low and there was no reduction in genetic diversity among zoeae. In principle, influxes of larvae from genetically distinct populations over 500 km to the north could have caused these differences; however, coalescent estimates indicated that gene flow from these distant populations has been very low and it is unlikely that first-stage zoeae would have been transported such great distances. The possibility remains that natural selection, directly or indirectly, is responsible for the observed patchiness in mitochondrial allele frequencies.