This study investigates the potential of the pet trade, particularly the conditions under which wild animals are captured and transported, to influence the community composition of the gastrointestinal flora and the prevalence of pathogens shed by Tokay geckos (Gekko gecko). The commensal enteric composition of individually housed Tokay geckos was characterized; and in an effort to understand the effects of importation on commensal enteric composition, experimental manipulations of density were conducted to mimic stressful overcrowding conditions in the pet trade. A total of 189 lactose-positive Enterobacteriaceae isolates were cultured from fecal samples obtained from 110 imported geckos. The top three most frequently cultured genera were Citrobacter (n = 114), Klebsiella (n = 29), and Enterobacter (n = 15). Citrobacter was the most frequently cultured genus from all geckos. The prevalence of Citrobacter spp. increased significantly from 55% among all individuals to 75% from grouped geckos (P = 0.011). The prevalence of Salmonella enterica subspecies arizonae, a common reptile-associated zoonotic pathogen, was ≤1% in individually housed geckos compared to 12% cultured from animals living in groups (P = 0.0004). The second most common genus cultured, Klebsiella, decreased significantly from 20% among individually housed geckos to 4% from all the combined animals (P = 0.007). The increase in prevalence of S. enterica subspecies arizonae and opportunistic pathogens like Citrobacter spp. illustrates that regulations aimed at decreasing overcrowding on imported reptiles might help to minimize pathogen shedding and transmission.