<p><strong>Background</strong>: Species of the <em>Fusarium</em> genus are considered as devastating phytopathogens of onion crops around the world. <strong>Objective</strong>:  This work aimed to know the causal agent of basal rot in onion crops from Puebla-México recorded in 2019. <strong>Methodology</strong>: The causal agent was isolated from diseased samples by tissue incubation in Potato Dextrose Agar medium (PDA) and the pathogenicity tests were done with the causal agent to demonstrate its involvement in basal rot. Monosporic cultures of the causal agent were generated for further microscopic characterization and molecular identification by Internal Transcribed Spacers ITS1 and ITS2. <strong>Results</strong>: According to the pathogenicity tests, the causal agent produced apical constriction and necrosis in the radicle and leaves accompanied by brown spots surrounded by yellowing as those observed in natural conditions. A 533 bp amplicon of the causative agent was obtained by partial amplification of the 5.8S rDNA gene. The sequence of the amplicon was compared with the sequences deposited in the database of the National Center for Biotechnology Information (NCBI) showing 100% homology with <em>Fusarium equiseti</em>. <strong>Implications</strong>: Our investigation reveals <em>F. equiseti</em> as an emergent causal agent of onion basal rot in crops from the community of “La Soledad” Puebla, México. <strong>Conclusion</strong>: Herein we report for the first time <em>F. equiseti</em> as a new phytopathogen of onion and further strategies should be considered for its control.</p>