Mycorrhizal symbioses, crucial for plant nutrition and ecosystem functioning, exhibit varying degrees of specificity between plant hosts and fungal symbionts. This study explores the genomic underpinnings of mycorrhizal fungal specificity, synthesizing recent advances in understanding the molecular mechanisms governing these intricate associations. Comparative genomic analyses of over 100 mycorrhizal fungal species have revealed that the loss of plant cell wall-degrading enzymes is a common feature, with ectomycorrhizal fungi retaining only 10-15% of these enzymes compared to their saprotrophic ancestors. This adaptation reflects the transition from saprotrophic to symbiotic lifestyles. Studies on effector proteins have identified several mycorrhiza-induced small secreted proteins (MiSSPs) that play key roles in symbiosis establishment. For instance, the MiSSP7 gene in Laccaria bicolor is essential for the colonization of Populus roots, highlighting the importance of effectors in host specificity. Genomic investigations have also uncovered expansions in certain gene families, such as those encoding for nutrient transporters, with some ectomycorrhizal fungi possessing up to three times more ammonium transporter genes than their non-mycorrhizal relatives. Furthermore, the analysis of plant genomes has revealed that up to 5% of plant genes are differentially expressed during mycorrhizal colonization, with common symbiosis genes being conserved across 80-90% of land plants. This study underscores the complex genomic landscape underlying mycorrhizal specificity, emphasizing the co-evolution of plant and fungal genomes. Future research directions include the functional characterization of candidate genes and exploration of epigenetic mechanisms in symbiosis regulation.