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Aim: To study the genetic variability and population structure of Colletotrichum species found to be associated with anthracnose of chilli in the north-eastern region of India. Methods and Results: Twenty-three Colletotrichum isolates were obtained from infected chilli fruits and leaves from the chilli growing regions of northeastern Uttar Pradesh, India, identified as Colletotrichum capsici and Colletotrichum acutatum using species-specific primers. Genetic variability among the isolates was analysed using RAPD and ISSR markers. The RAPD marker efficiently grouped the isolates at species level, while ISSR marker was effective in separating the isolates based on geographical origin. In vitro pathogenic test revealed the inability of C. acutatum isolates to infect unripe fruits, while C. capsici isolates were found to infect both ripe and unripe fruits at disease severity scale 7-9. Growth rate on different media was recorded to cross-confirm the classification of isolates, which clearly grouped the two species into distinct group on PCA plot. Conclusions: Two species, viz. C. capsici and C. acutatum, prevalent in the region were found to infect the fruits at postripening stage. Significance and Impact of the Study: The present study proposes the implementation of management strategies at postripening stages of the crop to control the spread of disease, thereby leading to increment in production of chilli in the given region. [ABSTRACT FROM AUTHOR]