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Abstract In Mexico, agave （ Agave angustifolia Haw.） crops stand out regionally due to their socioeconomic, agroecological and cultural importance. It is the most important raw material in the elaboration of two relevant alcoholic beverages: tequila and mezcal. Nevertheless, this crop is susceptible to phytopathological threats mainly fungi and bacteria, both having a massive impact in yearly production. In this paper, we describe an agave disease consisting in reddish chlorotic lesions along the leaf bases resulting in tissue degradation and producing soft rot （softening tissue and firmness loss）. Fast‐growing yellow and mucoid bacteria colonies were isolated from the lesions in BK agar. Microscopic analysis resulted in a Gram‐negative bacilli. Pathogenic tests resulted showed identical symptoms to the initial ones in natural maguey host plants as well as in the selected model Aloe vera L. showing more aggressive soft rot symptoms. It is important to highlight that in the selected plant model （ Aloe vera ）, the symptoms arose faster and more aggressively. Biochemical and molecular analysis of the bacterial isolate identifies it as Pantoea vagans, a species not previously documented in this crop. Although all bacterial infections in plants are treated in similar ways, accurate identification could translate into targeted prevention. The detection of Pantoea vagans is considered a relevant problem given the symptoms it causes. We conclusively reported a 37% infection incidence rate, which can mean significant economic losses. However, the role of the genus Pantoea in agave rot has been poorly studied. Therefore, this report shows the identification of a new Pantoea species bounded to agave cultivars in Malinalco municipality, state of Mexico.
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