Citrus tristeza virus (CTV) causes various syndromes of citrus and consists of diverse strains which may cause symptoms of differing severity. Lemon is the most important citrus crop produced in Tucumán province, Argentina, but the diversity of CTV strains within this region has been poorly studied. In this study we identified strains of CTV in lemons in 29 trees of five commonly planted lemon cultivars from this area using direct Sanger and next generation sequencing (NGS) of amplicons derived from the CTV p33 gene. The Kpg3/SP/T3 genotype was dominant in 28 of the 29 samples analysed, with one sample being dominant for a genotype of RB. This was confirmed with NGS in all but one instance. In addition, all thirteen samples tested by NGS were infected with RB, Kpg3/SP/T3 and HA 16–5 genotypes. One sample also had a minor VT component, while a further two samples also had a minor AT-1 component.