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Trichoderma species, through mechanisms such as mycoparasitism, antibiosis, induced resistance and competition, are able to suppress the growth and activity of soil microbes and therefore have the potential to influence ectomycorrhizal (ECM) fungal colonisation. ECM colonisation potential of Pinus radiata seedlings inoculated with the commercially available Trichoderma species bio-inoculant, ArborGuard™, was investigated in a commercial containerised nursery setting and in a separate glasshouse experiment. Application of ArborGuard™ to P. radiata seedlings in both the containerised nursery and glasshouse experiment had no detrimental effect on the ability of the naturally occurring ECM fungi to colonise the seedlings. Thelephora terrestris was the only ECM species colonising the P. radiata root tips in the containerised system while Tomentella ellisii was the dominant species found colonising the P. radiata root tips in the glasshouse experiment. No seedling growth promotion was observed with the addition of ArborGuard™. The results show that the Trichoderma bio-inoculant ArborGuard™ does not affect ECM colonisation of P. radiata seedlings by Th. terrestris and T. ellisii in a containerised nursery system.