To measure the left atrial (LA) function in patients with hypertrophic cardiomyopathy (HCM; with [OHCM] and without obstruction [NOHCM]) and hypertension-related left ventricular hypertrophy (H-LVH) using cardiovascular magnetic resonance imaging feature tracking (CMR-FT). Patients who met the criteria for HCM (n=68), H-LVH (n=46), and 30 healthy controls participated. Left atrial strain was analysed using CMR-FT in cine images with two and four chambers. The strain rate and LA strain measurements showed that patients with HCM, and H-LVH had impaired conduit and reservoir functions (versus controls). These capacities were more severely impaired in OHCM than those seen in NOHCM and H-LVH. The LA volume parameters (LAVIpac, LAVImin and LAVImax) from the OHCM group were higher than both the NOHCM and H-LVH groups (all p<0.05). There were differences between the OHCM and H-LVH groups in terms of the parameters for LA reservoir function (εs), booster pump function (SRa), and conduit function (SRe, LA passive EF, εe; p<0.05). The strongest correlations included the associations between LA total EF and εs, εe and LA passive EF, and SRe and LA passive EF. CMR-FT can reliably identify LA dysfunction and deformation in the early stages of HCM and H-LVH.