Mycoplasma conjunctivae is the etiological agent of infectious keratoconjunctivitis, a highly contagious ocular infection that affects both domestic and wild Caprinae species in the European Alps. In order to study the transmission and spread of M. conjunctivae across domestic and wild Caprinae populations, we developed a molecular method for subtyping and identifying strains of M. conjunctivae. This method is based on DNA sequence determination of a variable domain within the gene lppS, a gene that encodes an antigenic lipoprotein of M. conjunctivae. This domain of lppS shows variations among different strains but remains constant upon generations of individual strains on growth medium and thus allows identification of individual strains and estimation of their phylogenetic intercorrelations. The variable domain of lppS is amplified by PCR using primers that match conserved sequences of lppS flanking it. Sequence analysis of the amplified fragment enables fine subtyping of M. conjunctivae strains. The method is applicable both to isolated strains and to clinical samples directly without requiring the cultivation of the strain. Using this method, we show that M. conjunctivae was transmitted between domestic and wild animals that were grazing in proximate pastures. Certain animals also presented infections with two different strains simultaneously.Infectious keratoconjunctivitis (IKC) is a common, contagious ocular disease known as pinkeye of domestic small ruminants, particularly sheep and free-ranging Caprinae mainly in the Alps (13). This disease is characterized by inflammation of the conjunctiva and cornea. In the most-advanced stage, the cornea is opaque or even perforated (18), and blind wild animals may fall from cliffs or die from starvation. Mycoplasma conjunctivae is considered as the major etiological agent of IKC in Caprinae species such as alpine ibex (Capra ibex ibex) (13), alpine chamois (Rupicapra rupicapra rupicapra) (10,20), and mouflon (Ovis orientalis musimon) (23), as well as in domestic sheep and goat (15,16,25,26). In Switzerland, the prevalence of M. conjunctivae antibodies in adult sheep at the individual level was 53%, and the domestic sheep population was shown to act as a reservoir of the M. conjunctivae infection (15). In contrast, the M. conjunctivae infection is not selfmaintained in alpine chamois in eastern Switzerland and their infection may originate from domestic sheep living in proximity to chamois during the summer (12). Susceptibility of alpine ibex to sheep strains of M. conjunctivae was demonstrated by experimental infections, hence proving the possibility of transmission of mycoplasmal IKC between different species (13). This transmission of M. conjunctivae between domestic small ruminants and wild Caprinae may be caused by physical contacts and by flies acting as vectors between the species (11). In alpine regions, increases of IKC outbreaks are generally observed during the summer and autumn, which is coincident with the presence of domestic sheep grazing on alpine sum...