Pinus species are extensively abundant in Europe and, as pioneer trees, prominently influence local ecology. However, pine forests in Lithuania, Montenegro, and Ukraine have been significantly damaged by pine bark beetles (Tomicus sp.), which are closely associated with ophiostomatoid and other pathogenic fungi. This study aimed to identify the diversity of ophiostomatoid and other fungi associated with Tomicus sp. in these three countries. Fungi were isolated from beetles and identified. High-throughput sequencing of ITS2 rDNA yielded 285,828 reads, of which 91,141 high-quality reads were retained, representing 561 fungal operational taxonomic units (OTUs). The most important groups of fungi included ophiostomatoids, yeasts, and plant pathogens. While the fungal communities associated with Tomicus spp. were influenced more by environmental factors than by beetle species, the presence of known pathogens such as Ophiostoma spp. indicates that Tomicus spp. could play a significant role in dispersing harmful fungi. Although the virulence of these fungi may vary, their association with potentially pathogenic species suggests that Tomicus spp. may contribute to forest health decline, especially if environmental conditions or host susceptibility change.