Microbial model systems have made major contributions across the life sciences. Their influence extends beyond strictly microbiological research to inform and enhance general biological understanding. To cast light on how microbial populations and communities function as model systems, we examine their use in historical and contemporary research on evolutionary and ecological dynamics. We assess the pros and cons of microbial model systems, and identify specific ways in which they benefit research. Analyzing microbial model systems is of particular value as biologists become increasingly aware of the microbial world and its interactions with the rest of life.