San Bruno Mountain, a coastal site in California’s Mediterranean climate, is unique in combining long, dry, sunny summers with frequent and intense marine-layer fog, creating steep microclimate gradients. Fog moisture is important for epiphytic cryptogams (mosses and lichens that live on other plants), which cannot draw water from soil, yet these communities are poorly studied. We investigated the epiphytic cryptogam communities on coyote bush (Baccharis pilularis) using paired coastal and inland transects descending from the ridge summit to capture potential differences in fog exposure and resulting microbiomes. To record environmental conditions, we deployed microclimate dataloggers that recorded temperature and humidity through summer and fall, and calculated vapor pressure to estimate fog frequency and duration. We collected 10 coastal and 10 inland ~25 cm long branches and used string transects at 1 cm intervals to quantify visible epiphytes. We used microscopy, chemical tests, PCR (fungal ITS, algal 18S–23S, and bacterial 16S markers), followed by MinION nanopore sequencing to identify the moss, the fungal and photosynthetic partners of each lichen, and the associated microbiome of each specimen. Out of 693 lichen patches and 146 moss patches, we found differences in growth and community composition among the branches and transects for each lichen genera (13 observed), one species of moss (Pulvigera pringlei), and their microbiomes. By combining high-resolution microclimate monitoring with DNA sequencing, we demonstrate a powerful approach to link microclimate variation with cryptogam microbiome function in coastal ecosystems.