Since there is a limited knowledge about croatian populations of a carob tree (Ceratonia siliqua L.), a nutritively and protectively high-quality plant, this research was conducted to determine the morphological, genetic and phytochemical traits of the carob populations in Croatia. The morphometric investigations of carob were made on the samples of pods and leaves, while the genetic variability was determined using AFLP analysis of genomic DNA isolated from the leaf. The content of total phenols, flavonoids and tannins, as well as antioxidant potential of the pods and the leaves, was determined spectrophotometrically. Content of macro and microelements was determined by using ICP-AES techniques. The research revealed a significant variability of the morphological and phytochemical traits of pods and leaves of the investigated carob populations. A molecular AFLP analysis showed considerable variability in the studied populations, because the variance between individuals within a population is much higher (75.51%) than the variance between populations. Despite a significant statistical variability, UPGMA cluster analysis of the studied populations, can be grouped in the lowest degree of separation. The Mantel test revealed significant correlations between molecular, morphological and phytochemical properties of the pods and leaves in the studied populations. Populations of Vis, Šolta, Brač and Šipan have good morphological and phytochemical features of the pods. The pods of the populations Vis and Orašac have the highest antioxidant potential and are a good source of the minerals.