Abstract The spatial distribution of mycorrhizae and hyphae in a regolith of thin soils overlying deeply weathered granitic bedrock was investigated at Santa Margarita Ecological Reserve in southern California. The regolith supports mature Quercus agrifolia trees and consists of thin soils (24–100 cm) overlying four varieties of granitic parent materials, and a fault gouge. Evergreen plants with deep, extensive root systems are favored during inherent seasonal droughts of Mediterranean climate. However, sub-soil roots are confined to the fractures and are physically restricted from the matrix micropores of the weathered granitic bedrock where the bulk of the regolith plant available water exists. Ectomycorrhizal (EM) root tips were found throughout the regolith to depths of ∼4 m. Some EM infection frequencies of fracture-confined roots (range 1–63%) were similar to those found in the upper 30 cm of soil (range 33–94%). Hyphae were recovered from all depths and material types: soil (averaged 75.0–127.8 m cm −3), fracture (2.5–30.2 m cm −3), and matrix material (1.2–10.0 m cm −3). Hyphae in the form of rhizomorphs were also recovered from deep, matrix materials. Total N was extremely low in the fractures and negligible in the matrix materials; therefore we postulate that N deficits are not driving the formation of ectomycorrhizal infection within the bedrock. Hyphae have been shown to act as water conduits and can transport matrix water, otherwise unavailable to plants, from micropores to fracture-confined, mycorrhizal roots. The formation of mycorrhizae in weathered bedrock fractures, and hyphal extension into the matrix, may be crucial to the water balance of evergreen trees in Mediterranean climates by providing a link between matrix resources and the plant.