Swabs of conjunctiva were collected from 44 live and 226 hunter-harvested mule deer (Odocoileus hemionus) from Wyoming and Utah (USA). We identified 29 Gram negative and 22 Gram positive bacterial taxonomic categories, but many isolates from hunter-harvested animals were environmental contaminants. Staphylococcus spp. and Micrococcus spp. were the most common Gram positive bacteria isolated, and Enterobacter spp., Escherichia coli, and Pseudomonas spp. were common Gram negative bacteria isolated. Thelazia californiensis were found in 15% of hunter-harvested deer in Utah in 1994 and in 8% in 1995. Nematodes were found in 40% of live deer in 1995 and 66% in 1996. Three live animals showed clinical signs of infectious keratoconjunctivitis (IKC) in 1996, but pathogenic bacteria were not isolated from these individuals. Hemolytic, non-piliated Moraxella ovis was isolated from two clinically normal live deer in 1996 and isolates were similar to those cultured from IKC cases from Wyoming and Utah.