Anthracnosis and ramulosis are important diseases of cotton (Gossypium hirsutum), caused by Colletotrichum gossypii and C. gossypii var. cephalosporioides, respectively; both fungi seed transmitted. Ramulosis, also known as witch's broom, is considered to be more devastating, causing severe losses in several regions of Brazil where cotton is cultivated in large scale. It is difficult to detect both fungi in seed samples by conventional methods since the morphological variability between isolates within the same species makes detection unreliable. The goal of the presente work was to investigate the variation of 10 isolates of both fungi using DNA/RAPD markers. Part of the isolates was classified as C. gossypii and part as C. gossypii var. cephalosporioides, using the pathogenic test. The results showed that the biochemical markers used were not able to distinguish the isolates of anthracnosis from the isolates of ramulosis. On the other hand, the genetic similarity between the isolates demonstrated by RAPD analysis, was 51,78%, indicating the potential of this technique.
