Hybrid energy systems (HESs) generate electricity from multiple energy sources that complement each other. Recently, due to the reduction in costs of photovoltaic (PV) modules and wind turbines, these types of systems have become economically competitive. In this study, a mathematical programming model is applied to evaluate the techno-economic feasibility of autonomous units located in two isolated areas of Ecuador: first, the province of Galapagos (subtropical island) and second, the province of Morona Santiago (Amazonian tropical forest). The two case studies suggest that HESs are potential solutions to reduce the dependence of rural villages on fossil fuels and viable mechanisms to bring electrical power to isolated communities in Ecuador. Our results reveal that not only from the economic but also from the environmental point of view, for the case of the Galapagos province, a hybrid energy system with a PV−wind−battery configuration and a levelized cost of energy (LCOE) equal to 0.36 $/kWh is the optimal energy supply system. For the case of Morona Santiago, a hybrid energy system with a PV−diesel−battery configuration and an LCOE equal to 0.37 $/kWh is the most suitable configuration to meet the load of a typical isolated community in Ecuador. The proposed optimization model can be used as a decision-support tool for evaluating the viability of autonomous HES projects at any other location.