Information regarding the filamentous fungi and yeast microbiota on pear surfaces is limited when compared to other fruits such as grapes and apples. The effect of commercial postharvest practices on pear fruit surface microbiota and species composition is not known, particularly in terms of the presence of postharvest pathogens and potential biocontrol microorganisms. Pear fruit were collected at harvest in the orchards of four commercial farms, after harvest at a communal pack house following chlorine drenching and after modified atmosphere storage. Microbiological analysis showed that during season one the fungal populations on pears from the four farms were significantly lower after CA storage when compared to populations of orchard pears, however during season two, the opposite trend was observed. The yeast populations were either significantly higher or similar after CA storage compared to the orchard pear counts during both seasons. Commercial drenching led to either an increase or reduction in the filamentous fungi and yeast populations, however a definite trend could not be observed. The postharvest practices decreased the number of viable morphologically different yeast and filamentous fungal species. A total of 16 yeast and 24 filamentous fungal species were isolated. A 76% dominance of Ascomycetes was observed. Known postharvest pathogens Penicilium commune and Penicillium crysogenum were present after CA storage. Potential known biocontrol organisms included Aureobasidium pullulans, Cryptococcus sp. and Sporobolomyces roseus. Knowledge generated could contribute to development of commodity-specific supply-chain management systems and biocontrol strategies based on scientific data to reduce pear fruit losses and for quality control purposes.