Microbial colonization of the intestinal tract of commercial poultry is highly variable, likely due to the fact that poults and chicks are hatched and raised without exposure to adult birds and their microbiota. In industrial poultry production, it is hypothesized that most of the microbiota is obtained through horizontal transmission from the environment and very little by maternal transmission. The initial gut microbiota will therefore differ between flocks and companies based on environmental conditions at the hatchery. Day-old poults were collected from the hatchery of 2 companies at 3 different time points to monitor the initial colonizing microbiota by sequencing amplicons of marker genes for bacteria, lactic acid bacteria (LAB), fungi, and archaea. Bacterial colonizers were distinct by company (pseudo-F 38.7, P ≤ 0.05) with the predominant bacteria at Company A being clostridia, specifically Clostridium celatum group, C. paraputrificum, and C. tertium. Predominant bacteria at Company B were Enterobacteriaceae, belonging to 2 different groups, one that included Escherichia; Shigella and Salmonella and the other Klebsiella; Enterobacter; and others. The predominant LAB at both companies were Enterococcus faecalis and E. gallinarum, confirmed by sequencing the 16S ribosomal RNA (rRNA) gene of colonies picked from lactobacilli agar plate counts. The predominant fungi were Aspergillus niger and Saccharomyces cerevisiae, with Candida sake or Alterneria sp. in some samples of Company A. Archaeal sequences were detected only in a single poult from Company B. The initial gastrointestinal colonizers of poults vary across company and time, signifying a strong environmental effect on microbiota acquisition. There was an indication of maternal effects in certain breeder flocks from Company B. Further work is necessary to determine how this variability affects microbiota succession and impacts growth and production of the birds.