Shallot production has many challenges, including the anthracnose disease caused by the pathogen Colletotrichum gloeosporioides Penz. Disease characteristics include severe twisting of leaves, neck elongation, and necrosis of leaves. This disease can cause yield loss of up to 100 percent. In addition to chemical control practices, resistant shallot varieties will be very useful in decreasing losses. However, information about existing shallot varieties resistant to C. gloeosporioides is limited. The study objectives are to identify the shallot varieties resistant to C. gloeosporioides and identify morphological characters and secondary metabolites of the leaves that may associate with the defense mechanism in shallot. Fourteen shallot varieties underwent a single factor use in a randomized block design in the field and laboratory experiments. The experiment transpired from January to June 2021. Planting healthy shallot bulbs of all genotypes in a polybag containing sterile media continued by artificial inoculation of C. gloeosporioides after the plant had 3–5 leaves. The field test showed that the Sumenep variety has the best resistant level to C. gloeosporioides, with a disease severity score of about 30.19%. On the other hand, the Blue Lancor variety is most susceptible, with a disease severity score reaching 95.05%. The study also found an indication that a possible resistance of shallots to C. gloeosporioides relates to the thickness of the palisade tissue (r =-0.8, P < 0.001), with the induced mechanism associated with the detection of the presence and increase of carbamic acid concentrations.