The aim of this study was to assess the spoilage profile of half shell Pacific oysters (Crassostrea gigas) and Sydney rock oysters (Saccostrea glomerata) using 16S rRNA pyrosequencing to determine changes in the bacterial profile and identify any potential specific spoilage organisms for oysters. These profiles will provide detailed insight into the microbial ecology of shucked oysters during refrigerated storage. To provide context to the 16S rRNA pyrosequencing profiles, a microbial culture approach was used together with sensory evaluation and pH analysis.