Cenococcum geophilum Fr., one of several ectomycorrhizal species associated with black pine (Pinus thunbergii Parl.), is dominant in the coastal forests of Japan, even under adverse abiotic environmental conditions. In these forests, many tonnes of Sumipine® (fenitrothion) are applied every year to protect P. thunbergii from pine wilt disease, which is transmitted by a beetle. Here, we examined the effect of this insecticide on the species of fungi found as ectomycorrhizae on naturally regenerated P. thunbergii seedlings collected from coastal forest sites that had or had not been sprayed with fenitrothion. The proportion of C. geophilum ectomycorrhizae on black pine root tips was significantly higher in areas where fenitrothion had been applied than in areas where it had not. We measured the in vitro mycelial growth of C. geophilum as well as other ectomycorrhizal fungi of coastal black pine, Rhizopogon roseolus (Corda) Th. Fr. and Pisolithus arhizus (Scop.) Rauschert, at three levels of fenitrothion (density: 1.32 g/cm3), i.e., 0, 0.1 and 0.2 mL L−1. The growth of all three species decreased significantly as the fenitrothion dosage increased. However, the reduction of mycelial growth in response to fenitrothion was lower in C. geophilum than in the other two species. These results suggest that C. geophilum has a high tolerance for fenitrothion, which may explain its dominance over other ectomycorrhizal species in coastal forests in Japan where fenitrothion is routinely sprayed.