The present study was conducted to detect and identify the virus isolates and to determine the molecular diversity associated with CLCC-infected chilli plants grown in a wide range of agroecological zones in Sri Lanka over two consecutive cultivation seasons. Randomly-selected chilli plants showing virus-like symptoms were collected from five experimental sites representing different agroecological zones and symptoms were recorded. DNA extracted from the above chilli leaf samples were subjected to PCR amplification using JS35 F and JS36 R primers, which are specific to Chili leaf curl Sri Lanka virus (ChiLCSLV). Amplified PCR products which targeted a region of DNA-A genome of begomovirus were subjected to DNA sequencing. Subsequent DNA homology search identified virus isolates associated with the CLCC-infected chilli plants which gave the highest homology to chilli leaf curl Salem virus-India, chilli leaf curl-Bhavansagar-India, Pepper Leaf curl Bangladesh virus, ChiLCSLV-isolate 14, ChiLCSLV-isolate 15 and Tomato leaf curl geminivirus, but having a variation of percentage identity. Phylogenetic analysis confirmed the genetic divergence of the CL-14 and CL-15 isolates, being them more genetically closer to chilli leaf curl-Bhavansagar-India and chilli leaf curl Salem virus- India, respectively. Eventhough single nucleotide differences were found in different clades of virus isolates, there was no strong relationship with clade separation and the location or season from which the samples were collected. Clade separation also did not show a relationship with a particular type of symptom. Findings of the study clearly revealed the presence of a diverse number of begomovirus isolates associated with the CLCC-infected plants and the genomic variations of them.