Most eukaryotic species are colonized by a microbial community - the microbiota - that is acquired during early life stages and is critical to host development and health. Much research has focused on the microbiota biodiversity during the host life, however, empirical data on the basic ecological principles that govern microbiota assembly is lacking. Here we quantify the contribution of colonizer order, arrival time and colonization history to microbiota assembly on a host. We established the freshwater polyp and its dominant colonizer as a model system that enables the visualization and quantification of colonizer population size at the single cell resolution, , in real time. We estimate the carrying capacity of a single polyp as 2 × 10 cells, which is robust among individuals and time. Colonization experiments reveal a clear priority effect of first colonizers that depends on arrival time and colonization history. First arriving colonizers achieve a numerical advantage over secondary colonizers within a short time lag of 24 h. Furthermore, colonizers primed for the habitat achieve a numerical advantage in the absence of a time lag. These results follow the theoretical expectations for any bacterial habitat with a finite carrying capacity. Thus, colonization and succession processes are largely determined by the habitat occupancy over time and colonization history. Our experiments provide empirical data on the basic steps of host-associated microbiota establishment - the colonization stage. The presented approach supplies a framework for studying habitat characteristics and colonization dynamics within the host-microbe setting.