<p>The argan tree [<i>Argania spinosa</i> (L.) Skeels] is a multipurpose species endemic of Morocco. It has been mainly characterized as a self-incompatible (SI) species. Argan trees have been also identified in the Region of Murcia, located in Southeaster Spain, where they are in some cases currently yielding viable fruits and seeds in an isolated environment. This study investigates the self-compatibility (SC) of these Spanish argan genotypes. This was done through in situ research and characterization of isolated argan trees in open pollination settings. Additionally, the seedlings from these trees were characterized using (Simple Sequence Repeat) SSR markers. In addition, the ex situ study of the collection of Spanish argan genotypes from the CEBAS-CSIC (Centro de Edafología y Biología Aplicada del Segura—Consejo Superior de Investigaciones Científicas) in Murcia, have also been characterized in open pollination conditions and by bagging argan genotypes to evaluate fruit set in absence of pollinator also analysing the obtained seedlings by SSRs. As expected, in the analysis of in situ conserved argan genotypes, the isolated trees showed a suitable flowering intensity during the two years evaluated. While the Spanish argan genotypes isolated from ‘Cartagena’ and ‘Mazarrón’ showed fruits, the genotypes from ‘Molina de Segura’ and ‘Ojos’ showed a null fruit set in both years. In the case of bagging of these ex situ conserved genotypes, results showed that in the absence of natural pollinators of argan (especially flies), a certain level of fruiting is observed in bagged branches in some specimens. First analysis of seedlings through SSR markers showed that self-fertilization is possible in some argan genotypes and that fruits are obtained without pollen from other genotypes. If self-compatibility genotypes through pollinic tube analysis are confirmed in Spain or Morocco, they are very useful for basic research in breeding programmes.</p>