Oil-degrading bacteria and their communities have been in focus of the research for the past few decades for a number of reasons. First, this allows filling the voids in our knowledge on the major mechanisms facilitating the oil biodegradation, to identify the key organisms playing significant roles in these processes and, furthermore, to learn how to effectively manage their performance in situ to enhance the rates of biodegradation. Historically, of a particular interest for genomics studies were the so-called marine hydrocarbonoclastic bacteria, the petroleum biodegradation specialists with very restricted substrate profiles. Apart from their utility in environmental cleanup, oil-degrading bacteria possess an array of enzymes and pathways of a great potential for further biotechnological applications: biopolymers production, oxidation-reduction reactions, chiral synthesis, biosurfactant production, etc. In this chapter we describe current methods for genome and metagenome sequencing and annotation. Importantly, these are not limited to a particular group of microorganisms and are thus almost universally applicable. We focused exclusively on the methods and tools that everyone could use on a non-commercial basis. Due to the availability of numerous alternative methods and approaches, we have arbitrarily chosen reliable protocols that can be used by a common biologist without a great deal of computational biology background.