In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty demonstrated that DNA was the chemical basis of heredity and the genetic cornerstone of life on Earth (Avery et al., 1944). Some 30 years later, Frederick Sanger, Steve Nicklen, and Alan Coulson developed the dideoxy termination sequencing reaction to allow accurate and rapid determination of the sequence of long stretches of DNA (Sanger et al., 1977). Another 30 years later, we find that automated techniques, novel sequencing approaches, and technological advancements are again transforming our vision of the distribution and diversity of organisms. We have sequenced a human genome, several other animal and plant genomes, and over 500 complete microbial genomes. Sequencing the environment was the next big challenge, and marine microbiologists rose to that challenge. Here we review the current state and future prospects for marine environmental genomics.