The hoatzin (Opisthocomus hoazin) is a South American strict folivorous bird, with a crop microbial ecosystem that ferments dietary plants. Chicks progressively become independent from the adult-fed regurgitated crop liquids, and we hypothesized that the crop bacterial ecosystem develops through ecological succession mechanisms, as they grow into adults. The aim of this work was to compare the crop bacterial community in hoatzins from three age groups: newly hatched chicks, juveniles and adults by sequencing 16S rRNA genes and using the G2 PhyloChip. Cloning yielded a total of 2123 nearly full-length sequences binned into 294 operational taxonomic units (OTUs) (with <97% homology) belonging to 7 phyla, with 91% of novel OTUs. The microarray identified a diverse bacterial community dominated by Firmicutes and Bacteroidetes, with approximately 1400 taxa grouped in 40 phyla that included those detected by cloning. In comparison with the adult, the hoatzin chick crop had a greater abundance of Flavobacteriaceae, Clostridiaceae and Lachnospiraceae but lacked phyla DSS1, Deferribacteres and Termite group 1, which were mostly present in adults. The overall community structure of the crop of the hoatzin changes with age in a complex manner, probably responding to new niches made available through dietary changes related to the transition from dependent to independent feeding.