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ABSTRACT This study aimed to determine the main causes of low germination of Zanthoxylum rhoifolium Lam. (Rutaceae) seeds. Initially, the physical and physiological qualities were evaluated in seeds from four areas (lots) (Step I). Then, tests were performed (Step II) to determine physical dormancy (imbibition in water and methylene blue), physiological (germination test with scarification) and morphological (analysis of the embryo), in addition to histochemical analysis and (Step III) bioassay in aqueous and hydroalcoholic extracts. In Step I, a low germination was observed in all evaluated lots (≤ 1.0%); however, in the tetrazolium test, a high viability was verified for the Dois Vizinhos lot (88%). The lots showed differences in their physical aspects, with the predominance of seeds with damage. In Stage II, developed embryos were verified and there has no germination without the tegument. The methylene blue and histochemical test indicated the presence of an impermeable and thick tegmen. The bioessays with hydroalcoholic extracts indicated the presence of germination inhibitor(s). The main causes associated with low germination of Z. rhoifolium seeds are attributed to the combined dormancy due to an impermeable tegmen and some non-specific physiological dormancy, as well as the presence of damaged seeds. The seeds also contain germination inhibitors.