We present a comprehensive probabilistic seismic hazard study for Ecuador, a country exposed to a high seismic hazard from megathrust subduction earthquakes and moderate‐to‐large shallow crustal earthquakes. Building on knowledge gained during the last decade about historical and contemporary seismicity, active tectonics, geodynamics, and geodesy, several alternative earthquake recurrence models have been developed. We propose an areal seismic zonation for the seismogenic crustal, inslab, and interface sources, modified from Yepes et al. (2016), to account for the information gained after the 2016 7.8 Pedernales megathrust earthquake. Three different earthquake catalogs are used to account for uncertainties in magnitude–frequency distribution modeling. This first approach results in low hazard estimates for some areas near active crustal fault systems with low instrumental seismicity, but where geology and/or geodesy document rapid slip rates and high seismic potential. Consequently, we develop an alternative fault and background model that includes faults with earthquake recurrence models inferred from geologic and/or geodetic slip‐rate estimates. The geodetic slip rates for a set of simplified faults are estimated from a Global Positioning System (GPS) horizontal velocity field from Nocquet et al. (2014). Various scenarios are derived by varying the percentage of motion that takes place aseismically. Combining these alternative earthquake recurrence models in a logic tree, and using a set of selected ground‐motion models adapted to Ecuador’s different tectonic settings, mean hazard maps are obtained with their associated uncertainties. At the sites where uncertainties on hazard estimates are highest (difference between 84th and 16th percentiles ), the overall uncertainty is controlled by the epistemic uncertainty on the source model.