A collection of 55 bacterial isolates, mostly from roots (52%) or leaves/petioles (34%), and 60 fungal isolates, mostly from roots (78%) whereas none from leaves/petioles, was made from apple trees (Malus domestica) in Guelph, Simcoe and Vineland, Ontario. Half the bacteria were Bacillus species, and 60% of the fungi were Penicillium or Trichoderma species. However, the species were diverse in culture. For example, there were 7 colony types among 9 Bacillus aryabhattai isolates and 12 colony types among 16 Penicillium corylophilum isolates. For bacterial endophytes, 54 significantly inhibited growth of the apple scab pathogen, Venturia inaequalis in vitro, and the most effective was B. megaterium BRV13 with 100% inhibition. For fungal endophytes, 55 significantly inhibited growth of V. inaequalis in vitro, and the most effective was F. oxysporum FRS09 with 83% inhibition. This collection of endophytes shows that there is a diverse range of potential biological control agents for organic apple production.