Determining the genetic makeup of predominant microbial taxa with specific metabolic capabilities remains one the major challenges in microbial ecology and bioprospecting due to the limitations of current cell culturing and metagenomic methods. The complexity of microbial communities and intraspecies variation hinders the assembly of individual genomes from metagenomic shotgun libraries. Here we report on the assembly and analysis of the genome of an uncultured Flavobacterium from Gulf of Maine bacterioplankton. A single cell was isolated from a coastal water sample using fluorescence-activated cell sorting. Whole genome amplification via multiple strand displacement amplification was used to prepare sufficient DNA for constructing Sanger and 454 libraries. We will discuss assembly and analysis of the single cell sequence data with an emphasis on challenges unique to this type of data, limitations of the existing method and implications for future investigations of rare and unculturable microorganisms.