Micro-organism populations on the leaf surface can be an indicator of environmental health in orchards. A method was developed to detect changes in these populations in apple orchards. Firstly, the variation within orchards was investigated by sampling leaves from seven locations within four trees in spring and autumn. The population density and species richness of micro-organisms when grown on PDA showed tree and season effects (P < 0.05) but few significant effects of locations within trees or of replicated branches. Based on these findings, the method was modified to study phylloplane micro-organism populations in nine Canterbury orchards at four times during the 1999-2000 season. The method detected an increasing population density and richness (number of recognisable taxonomic units per sample) during the season in all orchards, and higher density and richness (P < 0.05) in unconventionally managed orchards compared with conventionally managed orchards.