Drought tolerance has been considered an important trait in sugarcane breeding programs, mainly to due the expansion of sugarcane cultivation to drought-prone environments. The aim of this research was to analyze the genetic variability of a panel of 88 sugarcane varieties phenotypically diverse for drought tolerance. Genetic dissimilarities were estimated based on 1839 molecular markers (TRAP and AFLP). The TRAP markers used were derived from genes related to sugar and drought tolerance metabolism. Dissimilarity measures were obtained as (1-SM), where SM is the simple matching similarity coefficient. The average dissimilarity was 0.33, indicating that there is still remained variability to be exploited. Complete linkage cluster analysis was performed considering the average dissimilarity as the threshold to establish the clusters. Ten groups were found. The varieties tend to be clustered according to the breeding programs that develop them. These groups could be clustered in two major groups, with old varieties and some plant introduction assigned to one cluster, and the newer varieties assigned to the other. Clustering differences occurred when the analysis was performed based only on different types of markers, what is expected, since different kinds of markers represent different levels of variability. However, some groups tend to be consistent in all situations. A larger number of groups (15) were found when the analysis was performed based on TRAP for drought tolerance, what can be explained by the low selection pressure applied to this trait until recently when compared with sugar content.