Recently, many bacterial genome and transcriptome studies have been performed based on the next-generation sequencing technologies. Therefore, how to select the appropriate research strategies is becoming increasingly important. In this paper, we discussed the research strategies of bacterial genome and transcriptome based on the next-generation sequencing technologies, and stated the opportunities and challenges in these fields briefly. We reviewed the conventional methods and procedures and presented the existing problems briefly for bacterial genome and transcriptome studies. The research strategies of bacterial genome and transcriptome provide a relatively complete pipeline for the majority of bacteria. Moreover, it will promote the research of other fields, such as the course of life, biological evolution, basal metabolism, disease and drugs.