The difference in species diversity on different substrates and the effect of both substrate (ground, logs, rocks, trees, and fallen branches) and site variation (such as disturbance history, aspect, slope) on bryophyte and lichen diversity were investigated in eastern Australian forests. Thirty-five sites in forest types ranging from dry sclerophyll to riparian were surveyed using a 50 m × 20 m area. Despite strong differences between the different substrates in species richness and composition for both bryophytes and lichens, differences within each substrate were limited. On examining each substrate separately, we found that variation in substrate quality, such as degree of log decay, was not strongly correlated with species diversity, explaining no more than 16% of richness and 5% of composition. Despite both bryophytes and lichens showing high fidelity for particular substrates, the quality of that substrate was not an important factor in determining species diversity in this study. Site environmental variables explained larger variation in both bryophyte and lichen species diversity, in particular species richness, with individual site variables explaining up to 41% of richness (topographic position) and 6% of composition (time since fire). For some site variables, notably some of the disturbance variables, there were no overall trends, but significant results for particular substrates, such as logging being significant only on logs and trees.