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Myocardial infarction (MI), caused by the occlusion of the left ventricular coronary artery, leads to the loss of cardiomyocytes and, potentially, heart failure. Cardiomyocytes in adult mammals proliferate at an extremely low rate and thus, a major challenge in MI treatment is supplementing exogenous cells and keeping them viable in MI areas. To address this challenge, injecting hydrogels encapsulating cells into MI areas, to compensate for the loss of cardiomyocytes, shows promise. This study synthesized two types of alginate hydrogels, based on self-crosslinking (SCL) and calcium ion crosslinking (Ca2+) in varying formulations. The hydrogels encapsulated living muscle-derived stem cells (MDSCs) and their performance was evaluated in terms of optimizing cell viability during the injection process, as well as the live/dead rate after long-term cultivation. The morphology of the hydrogel-encapsulated cells was characterized by scanning electronic microscopy (SEM) and live/dead cells were examined using an MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide staining) assay. The mechanical properties of the hydrogels were also determined via a rheometer, to identify their influence on cell viability during the injection process and with respect to long-term cultivation. The SCL hydrogel with a 0.8% alginate and 20% gelatin formulation resulted in the highest cell viability during the injection process, and the Ca2+ hydrogel composed of 1.1% alginate and 20% gelatin maintained the highest cell survival rate after two months in culture.