Borojo (Borojoa patinoi, Cuatrecasas), a rubiacea indigenous to the Colombian Pacific Region, produces a fleshy fruit having interesting nutritious characteristics making it a promising plant resource. It is used for fresh beverages; preserves and wine can also be obtained. It is an especially important source of income for some of the native population who sell it in local food markets and the main Colombian cities. Borojo is a dioecious plant; the two genders are not phenotypically distinguishable before flowering (3-4 years after planting). A non-selected plantation’s productivity thus becomes substantially reduced. This project was aimed at determining gender-linked amplified fragment length polymorphism (AFLP) markers. 20 and 22 bp primers were designed by sequencing one ofthesegender-linkedmarkersabdusedfordeterminingtheplants’genderviapolymerasechainreaction(PCR). Samples examined by PCR and AFLP were compared; the techniques presented no differences when determining plant gender. Determining gender in borojo is an important tool for agriculture because it allows adequate selection and distribution of female and male plants for establishing greater productivity plantations.