Abstract Indonesian has two prefixes, PE- and PEN-, that are similar in form and meaning, but are probably not allomorphs. In this study, we applied a distributional vector space model to clarify whether these prefixes have discriminable semantics. Comparisons of pairs of words within and across morphologically defined sets of words revealed that cosine similarities of pairs consisting of a word with PE- and a word with PEN- were reduced compared to pairs of only PE- words, or of only PEN- words. Furthermore, nouns with PE- were more similar to their base words than was the case for words with PEN-. The specialized use of PE- for words denoting agents, and the specialized use of PEN- for denoting instruments, was also visible in the semantic vector space. These differences in the semantics of PE- and PEN- thus provide further quantitative support for the independent status of PE- as opposed to PEN-.