Humans live in a world of diverse microorganisms, ranging from virus, to prokaryotes including bacteria andarchea, to eukaryotes including fungi and protists. Microorganisms have tremendous impact on human beings. While some microorganisms promote nitrogen fixation in important crops that feed humans, others can be deadly human pathogens that kill millions of people annually, still others cause harmful blooms. Microorganisms coexist with humans and can be also found in extreme environments such as hot springs and deep seas, as well as microenvironment inside humans, with some complex microbiomes that are critical to human health. With less than 1% of the microbial species are studied and known, microorganisms represent a large untapped resource. Genomic DNA contains ultimate hereditary information and dictates phenotypes. The advances of DNA sequencing technologies has made it possible to sequence and assemble genomes of thousands microorganisms. In particular, the emerging third generation sequencing technology led by Pacific Biosciences (PacBio) has addressed many challenging issues by providing long sequencing reads and high throughput capacity with its single molecule real time (SMRT) technology. PacBio DNA sequencing has not only driven the sequence and the assembly for complete genomes of microorganisms straightforward and affordable, but alsoenabled direct reading of various types of DNA methylation signatures in real time. Furthermore, PacBio DNA sequencing technology has been successfully applied to study metagenome of microbiomes. In this presentation, I will review progress in microbial genomics, reviewing progresses made in recent years, challenges and opportunities. I will also review efforts has been done in my research laboratory.