Gut microbial communities are known to be associated with immune defense. Changes to this microbial ecosystem can have negative effects on animal health. The Cleveland Metroparks Zoo has recently experienced an abnormally high mortality rate in their captive lorikeet colony, particularly in their younger animals. We hypothesized that lorikeet health may be associated with differences in gut microbial communities. We predicted that differences in gut microbiota between animals may be correlated with particular individual traits including bird age, sex, and species. Amplifying the 16S rRNA gene region of bacterial DNA and using a fragment analysis technique, we assessed gut microbial community structure across 34 birds. Analysis revealed two distinct groupings of similarly structured gut microbial communities across our samples; however, bird sex, age or species did not correlate with these groupings. In future laboratory studies, we will examine whether these two distinct groupings are driven by known deleterious microbes.