The phenotype via conventional cardiac MRI analysis of MYH7 (β-myosin heavy chain)- and MYBPC3 (β-myosin-binding protein C)-associated hypertrophic cardiomyopathy (HCM) groups is similar. Few studies exist on the genotypic-phenotypic association as assessed by machine learning in HCM patients. To explore the phenotypic differences based on radiomics analysis of T1 mapping images between MYH7 and MYBPC3-associated HCM subgroups. Prospective observational study. In all, 102 HCM patients with pathogenic, or likely pathogenic mutation, in MYH7 (n = 68) or MYBPC3 (n = 34) genes. Cardiac MRI was performed at 3.0T with balanced steady-state free precession (bSSFP), phase-sensitive inversion recovery (PSIR) late gadolinium enhancement (LGE), and modified Look-Locker inversion recovery (MOLLI) T1 mapping sequences. All patients underwent next-generation sequencing and Sanger genetic sequencing. Left ventricular native T1 and LGE were analyzed. One hundred and fifty-seven radiomic features were extracted and modeled using a support vector machine (SVM) combined with principal component analysis (PCA). Each subgroup was randomly split 4:1 (feature selection / test validation). Mann-Whitney U-tests and Student's t-tests were performed to assess differences between subgroups. A receiver operating characteristic (ROC) curve was used to assess the model's ability to stratify patients based on radiomic features. There were no significant differences between MYH7- and MYBPC3-associated HCM subgroups based on traditional native T1 values (global, basal, and middle short-axis slice native T1 ; P = 0.760, 0.914, and 0.178, respectively). However, the SVM model combined with PCA achieved an accuracy and area under the curve (AUC) of 92.0% and 0.968 (95% confidence interval [CI]: 0.968-0.971), respectively. For the test validation dataset, the accuracy and AUC were 85.5% and 0.886 (95% CI: 0.881-0.901), respectively. Radiomic analysis of native T1 mapping images may be able to discriminate between MYH7- and MYBPC3-associated HCM patients, exceeding the performance of conventional native T1 values. 3 TECHNICAL EFFICACY STAGE: 2. © 2020 International Society for Magnetic Resonance in Medicine.