Clavibacter michiganensis (Cm) is a tomato phytopathogenic bacterium. Outbreaks of Cm can result in severe yield and economic losses. To date, no resistance to Cm has been identified. Screening of wild tomato accessions has resulted in the identification of several sources of tolerance to Cm. The genetic background of tolerance provided by these sources is polygenic and complex. Previous results from advanced lines of a cross between Solanum arcanum LA2157 and S. lycopersicum showed that introgression lines carrying a locus of S. arcanum LA2157 on chromosome 7 had high levels of tolerance to Cm. We set out to functionally characterize this locus, in an effort to identify the gene(s) underlying the observed tolerance. Testing of near isogenic lines (NILs) containing a fixed LA2157 introgression on chromosome 7 did not lead to the expected results, as high susceptibility was observed in some NILs homozygous for the S. arcanum LA2157 allele. Therefore, we employed whole genome sequencing in combination with a bulk segregant analysis to identify loci involved in the observed tolerant phenotype. Our results suggest that two additional loci on chromosomes 2 and 4 together with the locus on chromosome 7 are required for tolerance to Cm.