Mycoplasma ovipneumoniae (Movp) is considered to be one of the most important mycoplasmas causing respiratory disease in small ruminants. Most epidemiologic and characterisation studies have been conducted on strains collected from sheep. Information on the presence and characteristics of Movp in healthy and pneumonic goats is limited. Phenotypic or genotypic differences between sheep and goat isolates have never been studied. The objective of our study was to characterise and compare the similarities and differences between caprine and ovine Movp strains isolated from affected and asymptomatic animals in order to elucidate phenotypic and genotypic variability. Four different techniques were used on a set of 23 Movp isolates. These included SDS-PAGE, Western blotting, random amplified polymorphic DNA and the heat shock protein 70 gene sequence-based method. A high degree of phenotypic and genotypic heterogeneity among Movp strains was demonstrated in this study. Our results demonstrated differences between goat and sheep strains, revealing not only a link between strains and host ruminant species, but by geographical origin as well. However, the finding of immunodominant antigens of molecular masses 36, 38, 40 and 70 kDa (±3 kDa) in Movp isolates from sheep and goats foretells their potential use in the development of serological diagnostic tests and vaccines.