Two methods are currently being used to describe ECM fungal communities associated with root tips: molecular techniques and morphological classification. Previous studies have found that these two approaches give conflicting results, with several fungal genotypes being identified from different ectomycorrhizas within the same morphotype. This has led researchers to question the usefulness of the morphological approach. The objective of this study was to compare the two approaches on ectomycorrhizas collected from three plant species growing in two different environments. Specifically, mycorrhizas were classified using a detailed morphological approach and then were subjected to PCR-RFLP analysis of the ITS region of the rRNA gene repeat. Ectomycorrhizas of Douglas-fir (Pseudotsuga menziesii) and paper birch (Betula papyrifera) were sampled from three widely dispersed sites with different soil types in the southern interior of British Columbia. Ectomycorrhizas of Douglas-fir and arbutoid mycorrhizas from Arctostaphylos uva-ursi were sampled from a fourth site in a different biogeoclimatic zone. For eight of eleven dominant morphotypes, one main RFLP banding pattern was observed. Ninety-three % of the mycorrhizas analyzed in these eight morphotypes would have been classified in the same way by either method. Five of the eight morphotypes were positively identified as Russula nigricans, Lactarius sp., Leccinum scabrum, Rhizopogon sect. Villosuli, and Thelephora terrestris by matching the RFLPs to those of fungal fruit bodies in our database or by sequencing the ITS region. The other morphotypes producing one dominant RFLP pattern were designated as Cenococcum, E-strain and Mycelium radicis atrovirens (MRA) based on their morphology. Morphotyping did not distinguish amongst major RFLP types for mycorrhizas classified as Amphinema-like, Piloderma-like and Rhizopogon-like A. We conclude that detailed morphological classification can be very useful as the primary method of ectomycorrhizal classification, when used in conjunction with molecular techniques. This approach will allow for an efficient use of research funds.