Chrysanthemum is ravaged by numerous agromyzid leafminers. Of which, Chromatomyia syngenesiae Hardy (Diptera: Agromyzidae) is an invasive polyphagous leafminer which causes heavy infestation by mining the green leaf tissue and weakens the plant by reducing the photosynthetic activity that results in unmarketable flowers. Hitherto, no further information is available from India on C. syngenesiae apart from just new record. The present study was undertaken to assess the damage potential and to identify the leafminer species attacking chrysanthemum. In this view, Survey was conducted in chrysanthemum growing polyhouse of Nilgiris, Tamil Nadu, India during 2016 to 2018. The results indicated that the damage potential caused by C. syngenesiae was 75.40 % and 69.00 % in 2016 to 2017 and 2017 to 2018, respectively. The highest parasitization of Diglyphus isaea (Eulophidae: Hymenoptera) Walker on C. syngenesiae was recorded as 18.27 % and 20.80 % in the respective years. In addition, C. syngenesiae and its parasitoid were characterized at molecular level and species specific DNA barcodes using mitochondrial Cytochrome Oxidase I (mtCOI) were developed. BLAST searching of GenBank showed 100 per cent sequence similarity with C. syngenesiae and clearly indicated the presence of C. syngenesiae at Nilgiris, Tamil Nadu, India. The sequences obtained from the present study was submitted to NCBI database as the first entry for species level representation from India and the accession numbers (C. syngenesiae -MN969922 and D. isaea - MN525179) were obtained.