The genus Dunaliella belongs to the division Chlorophyta and is known for its ability to survive in highly saline environments. Dunaliella is an important source of carotenoids, especially beta-carotene and has a wide range of applications. In this study, we aimed to isolate and identify Dunaliella strains from active and abandoned saltworks in Greece. Four seasonal samplings were carried out in seven active saltworks and two samplings were performed in an abandoned saltwork throughout the year 2020. Strains were characterized based on their morphological and phylogenetic traits, whilst their beta-carotene potential were evaluated. Fifteen (15) Dunaliella strains were isolated and classified into nine species based on morphological and morphometrical features. The isolated strains were assigned to different species such as D. parva, D. granulata, D. minuta, D. terricola, D. asymmetrica, D. bioculata, D. viridis, D. minutissima, and D. polymorpha. The results of the phylogenetic analysis indicate the formation of distinct clades among different Dunaliella species and suggest that morphological and morphometrical features may not always align with the phylogenetic position of species in the Dunaliella clade. Strains were found to produce a low amount of beta-carotene under default laboratory conditions. This study comprises the first phylogenetic inference of several Dunaliella species and highlights a gap on molecular data for Dunaliella spp. We provide valuable information on the diversity of Dunaliella strains in the saltworks of Greece, which can be used for further research and biotechnological applications.