Chilli or pepper leaf curl diseases have emerged over the last 10-15 years to be some of the most damaging constraints to Capsicum pepper production across much of Asia. The diseases are caused by begomovirus(es) (Whitefly-transmitted Geminiviruses) either as single infections or sometimes as mixed infections. Often in the field the diseases are combined with or confused with leaf curl or bunchy top caused by mites and/or thrips resulting in “Chillileaf curl complex”. So far, attempts to breed for resistance to Chilli leaf curl for this region have been largely unsuccessful because identified resistance has not been transferable to other locations or has broken down relatively quickly. Our aim in this study was to assess the diversity of begomoviruses able to infect chilli or sweet peppers across the region in order to identify a better strategy for identifying more durable leaf curl resistance and deploying it more sustainably.