Host-affiliated microbiomes are abundant and diverse in nature, but how they initially assemble is widely unknown. The squid-vibrio model system, where marine bacterium Vibrio fischeri colonizes Hawaiian bobtail squid Euprymna scolopes’s light organ, is utilized to study host-microbe symbioses. Here we report that co-isolated strains of V. fischeri’s ability to establish symbiosis in a single squid are likely due to each strain’s swimming ability in conjunction with when they initially encountered the animal.