Dunaliella salina has become the most important microorganism for the production of β-carotene around the world. Natural carotenoids are a source of active metabolites utilized in different areas of food nutrition and pharmaceuticals, both in humans and also in animals. Identification of Dunaliella species from natural environments or certified culture collections is not precise and it is time consuming. However, accurate identification is extremely important because a slight difference in Dunaliella species generates great differences in carotenoids production. Here, we describe an intron-sizing method to make a rapid and precise identification for each of the most important carotenogenic species, showing that each hyperproducer species has an exclusive 18S rDNA fingerprint profile.