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Brown rot is a common and devastating disease of different fruits and vegetables. During 2018, a profound brown rot was observed on lemon (Citrus lemon L.) in Islamabad, Pakistan and adjacent areas. This study was designed to identify disease causing pathogen of this disease. Diseased lemon fruit were collected from the orchards and disease causing pathogen was isolated. The morphology of pathogen was examined under stereoscope and compound microscope and the pathogen was identified as Alternaria alternata. For the molecular characterization of this fungus, 18S ribosomal RNA gene was sequenced and its phylogenetic analyses were performed. BLAST analysis revealed 100% similarity with A. alternate NS8, 18S ribosomal RNA gene, partial sequence (MK346034.1). This is the first report of brown rot of lemon, caused by A. alternata in Pakistan. For ecofriendly control of this disease, extracts of indigenous medicinal plants including Justacia adhatoda, Azadriachta indica, Foeniculum vulgare and Mentha spicata were used. In these plant extracts, the presence of various functional groups such as alcohols, carboxylic acids, esters, alkanes and alkenes was revealed by Fourier transform infrared spectroscopy (FTIR). Both in vitro and in vivo assay showed the significant role of aqueous plant extracts to suppress the growth of A. alternata. Among these phytoextracts, A. indica proved to be the most efficient in suppressing the growth of the pathogen and controlling disease. Findings of this study suggest the use of these plant extracts for environment friendly control of fruit rot disease. • Isolation of Fungi from lemon fruit. • Evaluation of pathogenicity of the isolated fungi. • Control of brown rot disease by using Phytoextracts. [ABSTRACT FROM AUTHOR]