Metagenomics, also called environmental-sequencing, is the study of microbial community sampled directly from their natural environment. Since the DNA sequences of various species are mixed up, it is very challenging for scientists to distinguish the species and the roles that they play in the environment. Therefore in metagenomics analysis, we are trying to answer two non-trivial questions: "who is there" and "what are they doing." In this talk I will briefly introduce the challenges that metagenomics brought to us and the computational methods that people use to tackle these problems. More specifically, I will introduce the "binning methods" that attempts to solve the "who is there" problem, and "functional analysis" for the "what are they doing" problem.