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Arbuscular mycorrhizal (AM) fungi have been on earth since 470 million years ago. AM fungi form mutualistic symbiosis with most terrestrial plants and thus, are thought to have played important roles in land colonization together with plants. In this thesis, I studied AM fungi in their natural habitat (Paper I and II) and examined their host preference (Paper IV). Further, I identified some genomic signatures of these obligate symbionts (Paper III). In Paper I, I studied soil communities of microeukaryotes in a protected grassland. Ribosomal DNA from soil samples was amplified (1500 bp) and sequenced with Pacific Bioscience technology. Three clustering methods were used to generate operational taxonomic units (OTUs). The three methods agreed on the effects of soil moisture and presence of Fritillaria meleagris on microeukaryotic communities but disagreed about specific compositions of these communities. Soil microeukaryotic communities were dominated by protists and AM fungi had a low abundance in spite of a high spore abundance. In Paper II, the genome of Funneliformis geosporum was successfully assembled from two spores isolated from the same field. This genome was compared with genomes of AM fungal taxa that had been maintained under controlled conditions for several years. Propagation under controlled conditions did not show to affect AM fungi genomes. In Paper III, I did comparative genomics and phylogenomics of AM fungi, making up the Glomeromycota phylum, and taxa from their sister lineages Mucoromycota and Mortierellomycota. The latter two phyla encompass taxa that are mainly saprotrophs, pathogens or facultative symbionts. For the first time, I rejected hard polytomy between these three phyla and demonstrated that Glomeromycota is sister to other two phyla. Further, I confirmed absence of genes involved in fatty acid synthesis and thiamine biosynthesis in AM fungi and showed that carbohydrate-active enzyme gene families were contracted in AM fungi. These findings can be regarded as genomic signatures of mutualistic lifestyle of AM fungi. In Paper IV, I performed a dual-host colonization experiment with leek and sorghum inoculated with Claroideoglomus claroideum. I found that symbiosis negatively affected sorghum fitness, as estimated by plant biomass but did not affect leek. Overall, this thesis highlights the difficulties associated with the study of AM fungi in complex soil communities or under controlled experimental conditions. Further, this thesis demonstrates how novel genomic methods can enhance our understanding about genome evolution of AM fungi, including field collected strains, in association with their lifestyle.