We used morphotyping and molecular methods to characterize ectomycorrhizas of bishop pine (Pinus muricata D. Don) and Bolander pine (Pinus contorta ssp. bolanderi (Parl.) Critchf.) from mixed conifer and hydric pygmy forests on the northern California coast. Sixteen ectomycorrhizal morphotypes were described, producing 15 internal transcribed spacer restriction fragment length polymorphism (ITS-RFLP) types, and 12 were identified via ITS sequencing. From a given site, all root tips of a specific morphotype produced identical ITS-RFLP patterns. However, sometimes two morphotypes produced the same ITS-RFLP type, and sometimes samples of the same morphotype from two different sites produced two different ITS-RFLP types. These results indicate that surveys of ectomycorrhizal fungi based on morphology alone are not sufficient, and that grouping morphotypes prior to molecular analysis can expedite the process. Ectomycorrhizas from mixed conifer included Russuloid sp., Tomentella sublilacina (Ellis & Holw.) Wakef., Tuber sp., and two Thelephoroid species. Ectomycorrhizas from hydric pygmy included two Dermocybe spp., a Cortinarius sp., two Thelephoroid spp., and Suillus tomentosus (Kauffman) Singer. Both plant communities contained Cenococcum geophilum Fr.:Fr. The hydric pygmy sites were more similar to each other than to the mixed conifer site (Jaccard similarity). The presence of ectomycorrhizal taxa in one plant community type may reflect biotic (host specificity) or abiotic (soil fertility or hydrology) adaptation.