Information on the prevalence of biofilm-related factors (PIA, Bhp, Aap, Embp) in Staphylococcus epidermidis of animal origin is scarce. In this study, 263 S. epidermidis isolates of diverse origin (animal, farmers, patients, and laboratory staff) were investigated for the presence of the ica operon (icaRADBC). The icaRADBC-positive isolates were further characterized by means of biofilm formation, presence of other biofilm-related genes, antimicrobial resistance, and population structure. Of all isolates, 28.5% (n = 75) were icaRADBC-positive, including 16.5% of animal origin, 29.1% farmer isolates, and 44.6% hospital-associated isolates (including patients and laboratory staff isolates). Most icaRADBC-positive isolates carried embp (n = 73), aap (n = 57), bhp (n = 22), and IS256 (n = 29). Statistical differences were found between animal and patient isolates for the presence of icaRADBC, bhp, and aap. No statistically significant relation was found between the presence of one or more genes and the level of biofilm formation. Most icaRADBC-positive isolates belonged to the clonal complex 5 (formerly 2) and most sequence types corresponded to types previously observed in community and nosocomial S. epidermidis populations. Although the prevalence of S. epidermidis in the nasal cavity of bovines and poultry is low, some isolates belong to STs related to ica-positive clinical strains.