Anthracnose caused by Colletotrichum sp. is an important disease causing severe damage to the quality and yield of cucumbers in the Mekong Delta of Viet Nam. This study was conducted to assess the genetic diversity of Colletotrichum isolates collected from the Mekong Delta using 13 random amplified polymorphic DNA (RAPD) and 10 inter-simple sequence repeat (ISSR) primers. In addition, associations between these molecular markers and pathogenicity were explored using stepwise multiple regression analysis (MRA). The molecular markers showed high percentages of polymorphic bands (71-100%). Similarity coefficients among the isolates (74-82%) derived from the combined RAPD-ISSR data indicated a moderate to high level of genetic similarity. Two isolates, DT and CT, had the highest similarity coefficients. A total of 13 significant alleles were found to be associated with disease severity and AUDPC indices. S1189-458 and ISSR848-675 were the most significant alleles associated with both disease severity and AUDPC indices. Overall, RAPD and ISSR markers are useful for assessing genetic diversity, while their association with pathogenicity requires further validation.