An understanding of factors influencing smallholder farmers’ livestock ownership at the household level is vital in formulating pro-poor livestock production policies and technologies. Hence, this study examined factors that influence livestock ownership of smallholder farmers. The data was collected randomly from three purposively selected study areas in the OR Tambo District (King Sabata Dalindyebo, Port St Johns and Ingquza Hill local municipalities) in the Eastern Cape Province of South Africa using a cross-sectional survey of 650 households. A multivariate probit model (MPM) was used to estimate correlates of livestock species ownership at the household level. Results indicated that education, age, household income, marital status, religion, rainfall, gender, household size and employment status influence livestock species ownership at the household level. Therefore, efforts to promote livestock ownership and production should be guided by these significant explanatory variables in the study area. Interdependence among species was also noted (cattle and sheep; goats and pigs; sheep and pigs; cattle and goats; goats and sheep), suggesting complementarity among the different types of livestock species. This complementarity among the species can possibly be explained by functional diversity generic with multi-species livestock farming which is worth supporting to enhance biodiversity conservation, climate change mitigation, rural resource use efficiency and socio-economic sustainability at the household level.