Abstract We present an approach for estimating in-situ relative permeability and capillary pressure through the joint inversion of array resistivity logging and formation test data. Considering a scenario of drilling a vertical well into an oil-bearing formation with water-based mud, the mud-filtrate invasion process can be regarded as a controlled experiment under reservoir conditions. Array resistivity logging can sense the formation resistivity perturbed by the two-phase flow invasion. Formation testing with fluid sampling can also provide information on the radially varying saturation and the associated changes in mobility, as well as information on the effect of capillary pressure. A facies-based workflow is developed to invert for the relative permeability and capillary pressure from the abovementioned two data sets. The inversion strategy is adjustable based on a sensitivity analysis as well as on the data available and the operational sequence of collecting the data. A hybrid inversion framework combining deterministic and stochastic optimization approaches is developed for the inversion of the data.