In animal-microbe symbioses, microbiome organization underpins established host behavior. Vast microbial populations can be inscrutable, so the simple symbiosis between marine bacterium Vibrio fischeri and Hawaiian Bobtail Squid Euprymna scolopes is utilized to elucidate host-microbe dynamics. Currently, squid microbiota composition is assessed by plating for CFU, which has quickly become antiquated to those probing the system. Here, we report the potential of leveraging qPCR to efficiently determine relative bacterial strain abundance in the squid-Vibrio system.