Myrciaria dubia, or camu-camu, is a perennial species that produces fruits of great nutritional interest because they have high levels of antioxidant compounds. The species occurs spontaneously on Amazonian river margins and requires a low amount of nutritional resources. Further, Myrciaria dubia fruits are collected via extractivism and managing this process is still at an incipient stage. The present study investigated the anatomical and histochemical aspects of the seeds of five clones of Myrciaria dubia. The external seed coat has an epidermis comprising a single layer of tabular cells that are rich in phenolic content, pectins, alkaloids, and terpenes. The cotyledons have a uniseriate epidermis, polyhedral parenchyma cells with a high concentration of starch grains, dispersed vascular bundles, alkaloids, and idioblasts with phenolic content, lipids, and proteins. The embryonic axis has a protoderm with cuboid, juxtaposed cells with thin walls and a conspicuous nucleus. Secondary metabolites in the seeds are mainly in the seed coat. This work provides new information about the anatomical and histochemical aspects of Myrciaria dubia seeds. No differences in the structural characteristics of the seeds and ovules were recorded among the clones since these are the most conserved reproductive organs in seed plants.