Fungi forming ectomycorrhizal (ECM) symbioses include numerous species spanning three major taxonomic divisions. Analysis of natural ECM fungal communities has traditionally been a highly-skilled, time-consuming process with heavy reliance on morphological characterization of the ECM root-tips through a combination of low- and high-magnification microscopic analysis. Gross morphological analysis of ECM root-tips, using dissecting microscopes only, later gained acceptance when supported by use of molecular methods such as PCR-Restriction Length Polymorphism to determine diversity within morphotype categories and correspondence between these categories. This approach allows researchers to avoid in-depth microscopic study of root tips and can be supported by restriction pattern databases and sequencing efforts. Morphotype methods allow for traditional quantification of ECM fungi based on numbers of root tips, a unit with functional significance. The molecular determination of ECM fungal types typically relies on the highly variable Internal Transcribed Spacer (ITS) sequences, ITS1 and ITS2, surrounding 5.8S-coding sequence and situated between the small subunit and the large subunit coding sequences of the ribosomal operon. Other ribosomal sequences, both genomic and mitochondrial, have also been used to determine ECM fungal types. Analysis of ECM root tips may also be achieved using current molecular methods for microbial community analysis such as Denaturing Gradient Gel Electrophoresis, Terminal Restriction Fragment Length Polymorphism and Length Heterogeneity PCR. These methods characterize both the types and, to some extent, relative abundances of fungi. Fungal community analysis approaches are also appropriate for analysis of extramatrical hyphae in the bulk soil, extending our capacity to study ECM fungal communities beyond the rhizoplane. The trend towards techniques that allow for larger sample sets without prohibitive labor and time requirements will permit us to more frequently address issues of spatial and temporal variability and better characterize the roles of ECM fungi in the environment.