Burrowing mammals are ubiquitous on farms in South Africa and can hinder agricultural practices. This study explored farmer perspectives of these species, and specifically the factors that influence these perspectives. Forty-four farmers responded to a questionnaire that assessed their ecological knowledge of, tolerance towards and lethal management of burrowing mammals that occur on their farms. The results from generalised linear models showed that neither farmer age, nor level of education are accurate predictors of ecological knowledge, overall tolerance towards burrowers, or their lethal management. Knowledge of burrowing mammals showed a significant relationship with tolerance, with more knowledgeable individuals displaying higher levels of tolerance. However, a farmer’s overall tolerance towards burrowing species did not affect the number of species managed. Our results also suggest that different values are attached to different species when it comes to lethal management. Thus, farmers commonly controlled the numbers of the problem rodent species, Highveld gerbil (Gerbilliscus brantsii) and Cape ground squirrel (Xerus inauris), but were less likely to manage black-backed jackal (Canis mesomelas) and warthog (Phacochoerus africanus), even when experiencing these as problematic. We suggest that the larger, more charismatic species possibly evoke more sympathy from farmers. Agro-ecosystems are likely to become increasingly important for conservation in the future, and we encourage continued studies on the environmental attitudes and approaches of agricultural practitioners as a means to understanding the current status and future trends in ecologically sustainable agriculture.