Metagenomics is revolutionizing the field of microbial ecology through techniques that eliminate the prerequisite of culturing. Metagenomic studies of microbial populations in different environments reveal the incredible diversity and adaptive capabilities of these organisms. With the advent of cheaper, high-throughput sequencing technologies, these studies are also producing vast amounts of sequence data. Here, we discuss the different components of a metagenomic study including sample collection, DNA extraction, sequencing, and informatics. We highlight their issues and challenges, and review the solutions that are currently in use. We conclude with examples of metagenomic studies conducted on environments of varying complexities.