There is little information about the amount of recent tuberculosis transmission in low-income settings. Genetic clustering can help identify ongoing transmission events. A retrospective observational study was performed on Mycobacterium tuberculosis isolates from persons living with HIV (PLHIV) and HIV-seronegative participants who submitted samples to a referral tuberculosis laboratory in Guatemala City, Guatemala from 2010 to 2014. Genotyping results were classified according to the international spoligotyping database, SITVIT2. Spoligotype patterns were categorized as clustered or nonclustered depending on their genotype. The proportion of clustering and the index of recent transmission index (RTIn-1) were estimated. In the RTIn-1 method, clustered cases represent recent transmission, whereas nonclustered cases represent reactivation of older tuberculosis infections. As a secondary aim, the potential risk factors associated with clustering in isolates from the subset of participants living with HIV were explored. From 2010 to 2014, a total of 479 study participants were confirmed as culture-positive tuberculosis cases. Among the 400 available isolates, 71 spoligotype patterns were identified. Overall, the most frequent spoligotyping families were Latin American-Mediterranean (LAM) (39%), followed by T (22%) and Haarlem (14%). Out of the 400 isolates, 365 were grouped in 36 clusters (range of cluster size: 2-92). Thus, the proportion of clustering was 91% and the RTIn-1 was 82%. Among PLHIV, pulmonary tuberculosis was associated with clustering (OR = 4.3, 95% CI 1.0-17.7). Our findings suggest high levels of ongoing transmission of M. tuberculosis in Guatemala as revealed by the high proportion of isolates falling into genomic clusters.