The mountain pine beetle (MPB), the most serious pest of lodgepole pine in mountainous western Canada, spread northeastward into lodgepole × jack pine hybrids in the boreal forest of Alberta in 2006. The MPB vectors three species of blue-stain fungi, which contribute to the success of the beetles. These fungi were isolated from MPB larvae and galleries in several lodgepole × jack pine stands in the Grande Prairie region of northwestern Alberta in autumn 2006 and winter and spring 2007. Fungi were recovered from more than 95% of gallery systems. The three fungi were similarly prevalent but Ophiostoma montium was the most frequently isolated fungus at each sampling point, isolated from 72% to 90% of gallery systems compared with 63% to 78% for Grosmannia clavigera, and 61% to 86% for Leptographium longiclavatum. Ophiostoma montium and G. clavigera were isolated from more larvae than gallery samples, with the opposite true for L. longiclavatum. Most gallery systems contained multiple fungi with three fungi per gallery system being more common in autumn and winter and two fungi more common in the spring. The combination of G. clavigera and L. longiclavatum was less common among gallery systems with two fungi than either of the pairwise combinations containing O. montium. Fungal prevalence was the same above and below snow level. The prevalence of the three fungi did not differ significantly among stands sampled in the spring but stands with more G. clavigera tended to have less L. longiclavatum. The winter of 2006–2007 was colder than average throughout Alberta with temperatures below −30°C in November, January and February, and all three fungi were present after the cold winter while most larvae had died, suggesting that overwintering mortality of the fungi will not limit persistence and spread of MPB in the boreal forest.