In February 2016, a fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,741 hectares of wheat crops with yield losses reaching up to 100% and affecting 20% of total wheat production of the country. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples directly collected from Bangladeshi fields. Population genomics analyses revealed that the outbreak was caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. We show that genomic surveillance can be rapidly established to monitor plant disease outbreaks yielding valuable information about the precise identity of the infectious agent.