The arrival order of colonists in developing populations can have a lasting influence on community and population structure, a phenomenon referred to as priority effects. To explore whether such priority effects are important in determining strain composition of populations of the cyanobacterium Microcystis, four Microcystis strains, isolated from a single lake and differing in functional traits, were grown during 4 weeks in the laboratory in all possible pairwise combinations, with the two strains either inoculated at the same time or with a time lag of 1 week, in the presence or absence of grazing Daphnia magna. The relative abundance of strains in the mixtures was assessed using denaturing gradient gel electrophoresis, and the growth rate of each strain in the mixtures was determined for the last 2 weeks of the experiment. We observed strong effects of inoculation order on the final population structure, and these effects were influenced by grazing Daphnia. The priority effects were strain-specific and occurred in two directions: some of the strains grew slower while others grew faster when inoculated second compared with when inoculated first. Our results indicate that priority effects may have a profound impact on strain composition of Microcystis populations.