Two hundred and thirty-seven species of macrofungi and 465 species of vascular plants were identified from seven selected permanent sites. Areas of permanent sites ranged from 0.5 to 10.8 ha. No fungal species were collected from all sites and 126 (53%) were collected from only one site. Fourteen fungal species (6%) were collected each year of the study and 116 (49%) were collected only 1 y. Numbers of newly collected fungal species from the seven sites did not decrease each year of the study. Classifying fungal genera by nutritional group showed 36% of the genera collected were terricolous, 53% lignicolous, 16% ectomycorrhizal and 5% parasites. Nine plant species were collected from all sites, while 232 (50%) were collected at only one site. Fifteen plant species on the sites are on the state list of rare, threatened and endangered species. Botany Bay, a narrow moist canyon with dense vegetation dominated by Picea glauca, Ostrya virginiana, Betula papyrifera and Pinus ponderosa, had the highest fungal and plant species diversity/ha of 188 and 238, respectively. Alabaugh Canyon, a dry open woodland dominated by Pinus ponderosa and Juniperus virginiana, had the lowest fungal and plant species diversity/ha of 3.1 and 14.7, respectively. Species diversity of all plants and all fungi at the sites had a very significant correlation (r  =  0.9). Regression and ANOVA showed a very significant relationship between species diversity of fungi and plants/ha (P  =  0.003). In cluster and principal component analyses assemblages of plants and fungi showed different patterns of similarity.