All ecosystems are composed of multiple species performing numerous functions. This plurality identified as biodiversity has become a research topic of general importance for understanding how ecosystems function. The word “biodiversity” has subsequently received different interpretations we aim to describe. Microbial systems can be used to illustrate these definitions and to clarify paradigms that have emerged in general ecology. Microbial biodiversity can be characterized by the kind of biodiversity (taxa or functional groups present), the representativeness of samples, and the culturability of samples or taxa, in terms of genetic, functional, or physiological characteristics. Biodiversity is a major driver of ecosystem functioning, and this relation is described in the case of several biotopes. Several mathematical approaches have been used to quantify microbial diversity, and the various indices are described and discussed.