ABSTRACT This paper proposed a new land cover mapping algorithm for remote sensing images under the presence of clouds. Here, we modelled the observed image as the weighted sum between the reflectances from the cloud-free image and clouds where weights depend on the degree of cloud contamination called the ‘cloud thickness’ map. Next, we represented the cloud thickness map using a level set function. Similarly, we also represented the land cover map as functions of different level set functions whose values indicate the class label. Next, the maximum a posteriori (MAP) criterion is employed where the most likely land cover and cloud thickness maps are chosen. Under the MAP criterion, the corresponding energy function whose values depend on the level set functions can be derived where the minimum energy point corresponds to the optimum land cover and cloud thickness maps. Since the level set functions are continuous, the optimum solution can be obtained by applying the calculus of variation where the gradient descent algorithm is employed. From the observation model, the cloud-free data can only be reconstructed only if thin to medium clouds are present since thick clouds can completely block the reflectance from the land cover materials. Thus, our algorithm is more suitable for thin to medium than thick cloud covers. Our synthesis and real cloud-contamination examples support our statement since our algorithm achieves significantly higher overall accuracies over other classification techniques, especially, in the thin to medium cloud contamination, and fails to recover the true land cover classes over the thick clouds.