Acute myeloid leukaemia (AML) is a genetically heterogeneous haematologic malignancy driven by the stepwise acquisition of chromosomal abnormalities and somatic mutations, resulting in clonal evolution. Current guidelines recommend integrating morphology, immunophenotyping, cytogenetics, and molecular analyses for disease classification and prognostic stratification. However, discrepancies between conventional cytogenetics and genome-wide approaches may occur. We describe a 70-year-old man presenting with severe pancytopenia, diagnosed with AML based on bone marrow morphology and immunophenotyping. Karyotyping revealed a deletion of chromosome 11 and additional material on chromosome 12. Targeted Next-Generation Sequencing identified pathogenic variants in FLT3, SF3B1, and EZH2, together with copy number losses involving chromosomes 7 and 11, the former not detected by chromosome banding analysis. To resolve this discrepancy, genome-wide Array-CGH+SNP analysis confirmed monosomy 7 and uncovered additional genomic abnormalities. Fluorescence in situ hybridization (FISH) validated chromosome 7 loss at the single-cell level. Taken together, these findings suggest that monosomy 7 was restricted to a leukaemic subclone underrepresented in metaphase analysis, likely owing to differential proliferative capacity among leukaemic populations. This case highlights how integrated cytogenomic profiling can uncover clinically relevant clonal heterogeneity missed by conventional cytogenetics alone, refining ELN risk stratification and underscoring the value of combining chromosome-based and DNA-based technologies in AML.