In a field experiment comparing the effect of treatment with Bacillus thuringiensis (Bt) and the pyrethroid insecticide, cypermethrin, on leaf microflora across the growing season, no significant differences were found, apart from more bacteria on cypermethrin-treated leaves on 24 September (P < 0·05). No effect was seen on fungal diversity or numbers. In contrast, the pyrethroid insecticide inhibited growth of 44% of bacterial isolates tested in vitro; Bt was not inhibitory. Bacillus thuringiensis numbers on treated leaves increased throughout the season, following repeated applications.