Advances in metagenomics and genome recovery from diverse habitats have dramatically ex- panded the availability of microbial genomes, unlocking unprecedented insights into microbial ecology and evolution. These discoveries are paving the way for transformative biotechnolog- ical and biomedical innovations. Despite this progress, final genome collections often provide an incomplete picture of microbial diversity, limiting our understanding of genome variation and excluding certain gene family orthologs. In contrast, metagenomic assemblies offer a more comprehensive view of microbial genomic diversity, capturing gene families lost during genome recovery and revealing broader ecological and variation of orthologs. This thesis in- troduces the EcoPhylo workflow, an open-source computational framework designed to track the phylogeography of gene families across environments. By leveraging single-copy core genes, such as ribosomal protein gene families, EcoPhylo enables benchmarking of genome recovery rates across environments, taxa, and recovery methods, providing a powerful tool for evaluating microbial genome datasets. Using this workflow, I benchmarked genome re- covery rates in the human oral cavity and gut, uncovering variation across taxa and biomes, and offering valuable guidance for optimizing genome recovery strategies in future studies. The scalability of EcoPhylo is further demonstrated through its application to a biome-level genome collection from the global surface ocean, highlighting its ability to analyze large-scale datasets. Additionally, I applied EcoPhylo to investigate the evolutionary landscape of anaero- bic flavin respiratory reductases across hundreds of gut microbes, illustrating its broader utility for exploring gene family phylogenetics and functional diversity. Overall, the EcoPhylo work- flow provides a platform for linking microbial genomes and gene families across environmental metagenomics datasets and offers a new avenue for benchmarking genome recovery efforts and advancing our understanding of microbial ecology.