A quick search of the Genbank nucleotide database for the word “soil” retrieves over 430,000 entries. This collection of genetic information reflects the enormous diversity of life in soil. Microbial ecology is the study of the interactions between microorganisms within an environment, and DNA sequencing is a vital tool for understanding these interactions. Although, there are many ways DNA sequences collected from soil are used, I will focus on two general strategies for applying sequence information for microbial ecology studies of soil. The first strategy is to catalogue microbial diversity, which includes identifying dominant and functionally important organisms, and monitoring community changes. Techniques like T-RFLP and DGGE are commonly used to compare microbial diversity between environments and to monitor community changes. Although these techniques rely on sequence variations between species, no technique yields as much bulk information as DNA sequencing itself. Once a target gene has been sequenced, it can be compared to sequence databases for identification and can be used to infer phylogenies. I will present some of the strategies used to obtain DNA sequences from soil microorganisms and discuss how sequence data is used to describe species diversity in soil using 16S rRNA and ecotype-specific functional genes. The second strategy is microbial genomics, which involves searching sequence information to uncover the genetic basis for microbial activities. As sequencing technologies improve and computing power increases, longer, more accurate, sequence data is becoming available. It is now possible to generate complete genome sequences for individual organisms and even to collect whole-environment genome sequence information. Like the human genome project, genome sequencing from microorganisms is providing a vast amount of information about microbial physiology, ecology, and evolution. I will review how microbial genomics is being used to identify new genes for novel microbial products and processes.