Feijoa sellowiana (O. Berg) is a broadly widespread fruit tree species at a very early stage of domestication. Although appreciated for its flavored berries rich in nutrients and nutraceuticals, and as an ornamental plant, feijoa is still considered an underutilized species and little information is available about its genetic background, cultivar traceability and divergence. This study aimed to investigate, for the first time, the genetic diversity of feijoa through the application of AFLPs. Specifically, twenty cultivars from different countries and six wild types (WTs) from their area of origin (Misiones, Argentina) were analyzed. The AFLPs proved to be informative, revealing the values of the percentage of polymorphic loci (PPB), Nei’s genetic diversity (h), and the Shannon index (I) at 69.36%, 0.27, and 0.43, respectively, consistent with the average of long-lived perennial and outcrossing species. However, despite the limited number of WTs examined, the genetic variability (h) was higher (approximately 37%) within the six samples compared to cultivars. The population structure analysis identified three clusters, with WTs forming a separated cluster (III) as expected. Cultivars were divided into two clusters (I and II), with cluster I exhibiting a closer genetic proximity to WTs compared to cluster II. This finding was further confirmed using the UPGMA dendrogram based on Provesti distances. This work raised awareness of the genetic variability among the feijoa’s widespread cultivars and demonstrated that the limited genetic breeding programs over the last decades resulted in low diversity among them. Moreover, these results confirm the hypothesis that all varieties are derived from a single narrow ancestral population. The potential of this species is considerable and needs to be further investigated to exploit its peculiarities.