Rock lobsters of the Palinuridae are the most valuable wild fisheries sector in Australia and are currently target aquaculture species. Significant challenges exist however to produce commercial scale quantities of post-larvae due to an extended larval phase which acerbates a high rate of larval attrition caused by inadequate nutrition and a challenging microbial environment. Here we investigate a diverse and varied bacterial community in four compartments of the larval-rearing system: the water column, the biofilm, live feeds and the phyllosomas themselves. External fouling of phyllosoma by filamentous Thiothrix sp. was documented by scanning electron microscopy (SEM) and fluorescence in situ hybridisation (FISH). Internal proliferation of bacteria coinciding with mass mortality of phyllosoma was observed in histopathological analysis and identified as Vibrio sp. by specific labelling of sectioned hepatopancreas tissue using FISH. Of particular interest in relation to larval mortalities was a range of Vibrio species, isolated from the four rearing compartments, closely affiliated with V. alginolyticus, V. parahaemolyticus, and V. harveyi. The presence of bacterial quorum sensing signal molecules within the system was demonstrated in both biofilm and phyllosoma environments during a larval-rearing run. Interestingly, a large increase in quorum sensing signal molecules was detected in phyllosoma corresponding with mass mortality.