The aim of this paper is to compare the socio-spatial patterns of innovation and knowledge linkages of a biopharmaceutical and an agro-food biotech cluster. Dissimilarities can be expected based on differences in terms of historical technological regimes and sectoral innovation system dynamics between the agro-food and pharmaceutical industries in general and particularly the distinctive analytical (science-based) knowledge base of biopharmaceuticals in contrast with the more synthetic (engineering-based) knowledge base of agro-food biotechnology. Drawing on bibliometric data and case material the study compares two representative bioregions: a biopharmaceutical cluster in Scania, Sweden and an agro-food biotech cluster in Saskatoon, Canada. The empirical study supports the theoretical expectations and shows that knowledge dynamics in the agro-food cluster are more localized than in the biopharmaceuticals cluster. It is important, however, to acknowledge that these differences are relative. Both sectors display local and non-local patterns of collaboration following the general pattern for biotechnology.