Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecologyand evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a newand accurate method, CLONCASE, for estimating both the rate of sexual vs. asexual reproduction and the effective populationsize, based on the frequency of clonemate resampling across generations. Simulations showed that our methodprovides reliable estimates of sex frequency and effective population size for a wide range of parameters. The CLONCASEmethod was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an importantwheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using twotemporally spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e. threequarterof individuals being sexually derived during the yearly sexual cycle), indicating strong contribution of sexualreproduction to the life cycle of the pathogen in this area. The inferred effective population size of this partially clonalorganism (Nc = 998) was in good agreement with estimates obtained using methods based on temporal variationsin allelic frequencies. The CLONCASE estimator presented herein is the first method allowing accurate inference of bothsex frequency and effective population size from population data without knowledge of recombination or mutationrates. CLONCASE can be applied to population genetic data from any organism with cyclical parthenogenesis andshould in particular be very useful for improving our understanding of pest and microbial population biology.