Chemical variation of Silybum marianum growing in the north, middle, and south of Egypt was investigated. Variation was assessed according to the content of the individual silymarin components in the fruits of the plant. The fruits were distinguished according to location, plant variety, and fruit color (maturity). Accelerated solvent extraction was used to standardize the silymarin extraction. Quantitative analysis of the content of silymarin components was carried out using HPLC with qNMR-controlled reference standards of taxifolin and seven major flavonolignans including silybin A, silybin B, isosilybin A, isosilybin B, silychristin, isosilychristin, and silydianin. The quantification method was validated in accordance with ICH guidelines. Principal component analysis and hierarchical clustering were carried out to create homogeneous clusters of samples based on the content of the silymarin components. Taxifolin had the lowest correlation relative to other silymarin components, whereas silybin A was positively correlated with silybin B. The samples clustered into three classes: silydianin-rich samples, samples with an average silymarin content of <18.8 mg/g, and one class enriched in silymarin (>18.8 mg/g). S. marianum growing in the Nile delta showed the highest silymarin content. No correlation was found between fruit color and silymarin content, indicating that the fruit maturity stage has no significance.