BackgroundChina is a country with a high burden of tuberculosis (TB). TB outbreaks are frequent in schools. Thus, understanding the transmission patterns is crucial for controlling TB.MethodIn this genomic epidemiological study, the conventional epidemiological survey data combined with whole-genome sequencing was used to assess the genotypic distribution and transmission characteristics ofMycobacterium tuberculosisstrains isolated from patients with TB attending schools during 2015 to 2019 in Guangzhou, China.ResultThe TB incidence was mainly concentrated in regular secondary schools and technical and vocational schools. The incidence of drug resistance among the students was 16.30% (22/135). The phylogenetic tree showed that 79.26% (107/135) and 20.74% (28/135) of the strains belonged to lineage 2 (Beijing genotype) and lineage 4 (Euro-American genotype), respectively. Among the 135 isolates, five clusters with genomic distance within 12 single nucleotide polymorphisms were identified; these clusters included 10 strains, accounting for an overall clustering rate of 7.4% (10/135), which showed a much lower transmission index. The distance between the home or school address and the interval time of symptom onset or diagnosis indicated that campus dissemination and community dissemination may be existed both, and community dissemination is the main.Conclusion and recommendationTB cases in Guangzhou schools were mainly disseminated and predominantly originated from community transmission. Accordingly, surveillance needs to be strengthened to stop the spread of TB in schools.