Morphological characterization of habanero pepper (Capsicum chinense Jacq.) showed that chilli fruit occasionally contains a small internal fruit (SIF) developing inside the main fruit. SIF morphology showed a normal fruit with pericarp, two locules and small reminiscent ovules joined to placental-like tissues. Histological analysis showed that SIFs maintain physical connexion with the placental tissues of the main fruit through vascular tissues. A Hardy-Weinberg analysis suggested that the frequency of SIF formation in the Capsicum chinense population studied is not the result of natural selection. This is the first report on this morphological abnormality in Capsicum chinense and constitutes an initial attempt to explain SIF formation frequency in this chilli pepper.