Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub lineages of MTB and their transmission patterns.DNA was extracted from 89 isolates of MTB collected during 2012 and 2013 from new pulmonary tuberculosis patients in Kandy, Sri Lanka and analyzed by spoligotyping, large sequence polymorphism (LSP), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and drug resistance-associated gene sequencing.The predominant lineage was lineage 4 (Euro-American, 46.1%), followed by lineage 1 (Indo-Oceanic, 29.6%), lineage 2 (East-Asian, 23.6%) and lineage 3 (Central-Asian, 1.2%). Among 26 spoligotype patterns, eight were undesignated or new types and seven of these belonged to lineage 4. Undesignated lineage 4/SIT124 (n = 2/8) and SIT3234 (n = 8/8) clustered together based on 24-locus MIRU-VNTR typing. The dominant sublineage was Beijing/SIT1 (n = 19), with isoniazid resistance katG G944C mutation (Ser315Thr) detected in two of them.The population structure of MTB in Kandy, Sri Lanka was different from the South Asian Region. Clonal expansion of locally evolved lineage 4/SIT3234 and detection of the pre-MDR Beijing isolates from new TB patients is alarming and will require continuous monitoring.