Mycoplasma agalactiae is the main causal agent of contagious agalactia syndrome in Spain. It is a severe disease of small ruminants, endemic in Mediterranean countries, that is characterized by mastitis, arthritis, and keratoconjunctivitis. This paper investigates the temporal, spatial, and host-related factors in the distribution of M. agalactiae infection from October 1996 to November 1998 and March 2002 to May 2003 in Spanish ibex (Capra pyrenaica) populations from Andalusia, in southern Spain. The predisposing factors to infection among previously selected factors (year of sampling, climatic season, geographic origin according to province, mountain range and metapopulation, sex, year of life, presence of scabies, and phase of the reproductive cycle) were established. We collected conjunctival and ear-canal swabs from 411 free-ranging ibexes. The frequency of infected ibexes was 11.2%. The peak frequency of infection occurred in 1998 and in summer. Granada was the province with greatest risk (odds ratio=2.6) of carriers (18.8% infected). The predisposing factors were sex (females), age (young animals), and metapopulation (Sierra Nevada). We identified a higher number of infected ibexes in the metapopulation “Sierra Nevada” (34/256) and significant differences among the three established metapopulations (P<0.01). Mycoplasma agalactiae infection represents a risk for population density and maintenance of these wild populations; infections can result in blindness, malnutrition, and polyarthritis leading to numerous deaths.