Colorectal cancer (CRC) is the third most common cancer worldwide. The disease is characterized by a high level of (epi-) genetic heterogeneity, with on average 93 exonic mutations in non-hypermutated and several 1000 exonic mutations in hypermutated tumours, as well as genome-wide DNA hypomethylation and focal hypermethylation at CpG islands. A subset of tumours is thought to be characterized by a particularly pronounced CpG island methylator phenotype (CIMP+ve). In addition, it is becoming increasingly apparent that CRCs show a high degree of intra-tumour clonal diversity. Much of the latter data are derived from comparisons of primary cancers and matched metastatic lesions, but the analysis of clonal structures within tumour bulk remains challenging. Molecular tumour heterogeneity has major implications for tumour prognosis and treatment response. Here, we analyzed human CRC cell lines as a model system for tumour bulk (epi-) genetic heterogeneity. We generated a series of six subclones for four CRC cell lines by single cell flow cytometry sorting, selected to represent hypermutated/non-hypermutated and CIMP-ve/CIMP+ve cases. We then performed genome-wide DNA methylation array analysis and targeted next-generation sequencing on a panel of 160 genes commonly mutated in cancer. Our data highlights the existence of pronounced clonal substructure at both the genetic and epigenetic level in CRC. Furthermore, we show that this clonal substructure translates into differential therapeutic responses when treated with DNA damaging drugs.