During a field survey in Tamil Nadu (2014–16), chilli plants showing chlorotic and necrotic ring spots and necrotic streaks on leaves and stems were observed. Disease incidence ranged between 5 and 50% among five surveyed districts. RT-PCR assay using species specific primers detected 25% of samples infected with Capsicum chlorosis virus (CaCV) and 50% of samples infected with groundnut bud necrosis virus (GBNV). For simultaneous detection of CaCV and GBNV, duplex RT-PCR (dRT-PCR) has been validated. Complete nucleotide sequences of L-RNA, M-RNA, NSs and N genes of CaCV isolate (CaCV-TN-CBE) were determined.The L-RNA constitutes 8913 nt, M-RNA of 4848 nt, NSs gene of 1320 nt and the N gene of 828 nt. Sequence analysis showed that CaCV-TN-CBE isolate is closely related to China isolate based on L- and M- RNA whereas with Taiwan isolate based on S RNA. Also, based on nucleotide identity and phylogenetic analysis CaCV-TN-CBE isolate is different from the previously reported isolate from India. Further nucleotide sequences of L- and S- RNA have shown recombination events. This study suggested the isolate infecting chilli in Tamil Nadu might have evolved by undergoing recombination and reassortment evolutionary mechanisms.