Silybum marianum (L.) Gaertner. (milk thistle), is a member of the Asteraceae family. Silymarin has hepatoprotective effects, accumulates at high levels in the external cover of milk thistle seeds, and is composed of flavonolignan isomers. In the present study, we assembled and annotated the mitogenome of Silybum marianum. This mitogenome was found to have a length of 407,123 base pairs and an overall base composition: A, 27.41%; T, 27.33%; G, 22.72%; and C, 22.54%. Seventy-four unique genes were identified in the Silybum marianum mitogenome based on annotation results, including 27 protein-coding genes, 44 tRNA genes, and 3 rRNA genes. Common protein-coding genes of 11 Asteraceae family references and four outgroup (Campanulaceae and Solanaceae) mitogenomes were used to construct a phylogenetic tree. The phylogenetic tree of the Silybum marianum mitogenome revealed close relationships with three reference mitogenomes (Arctium tomentosum, Arctium lappa, and Saussurea costus), and the flower morphology of Silybum marianum was similar to that of the three reference mitogenomes. This report describes unique features of the Silybum marianum mitogenome relative to the three related reference mitogenomes. In addition, we could envisage a specific analysis of the phylogenetic relationship of Silybum mariaum using additional Asteraceae family mitogenomes.