Chili can be infected by Begomovirus through whiteflies (Bemisia tabaci) serving as a vector insect. Begomovirus infection causes dwarf plants and yellow curly leaves. The molecular detection of Begomovirus coat protein gene may serve as a preliminary identification of Begomovirus. This study was conducted to observe the differences in the symptom severity of Begomovirus infection in chilies (Capsicum frutescens L. ‘Cempluk’) planted inside and outside a screen house. This study also observed whether or not using a screen house in chili farming affects the diversity of the coat protein of Begomovirus. Symptom observation and sampling were conducted in Madurejo, Prambanan, Sleman. Molecular detection was performed by amplifying the coat protein (CP) gene using the universal primer Krusty and Homer. Results showed 7 plant samples with DNA bands ± 550 bp and confirmed that the plants were positively infected with Begomovirus. The amplified bands were purified and sequenced. The nucleotide sequences were analyzed using BLASTn, followed by phylogenetic analysis using MEGA. Planting chili in the screen house resulted in low disease severity and good crop conditions. The coat protein sequence showed different strains of Begomovirus infected the chili plants inside and outside the screen house. Pepper yellow leaf curl Indonesia virus (PepYLCIV) was found inside the screen house while PepYLCIV [Ageratum] was dominant outside the screen house. Both strains are closely related to other Pepper yellow leaf curl virus (PepYLCV) from various regions in Indonesia. Optical manipulation using an ultraviolet screen or screen house was effective in reducing Begomovirus infection and improving plant performance.