Recombination events complicate the evolutionary history of populations and species and have a significant impact on the inference of isolation-with-migration (IM) models. However, several existing methods have been developed, assuming no recombination within a locus and free recombination between loci. In this study, we investigated the effect of recombination on the estimation of IM models using genomic data. We conducted a simulation study to evaluate the consistency of the parameter estimators with up to 1,000 loci and analyze true gene trees to examine the sources of errors in estimating the IM model parameters. The results showed that the presence of recombination led to biased estimates of the IM model parameters, with population sizes being more overestimated and migration rates being more underestimated as the number of loci increased. The magnitude of the biases tended to increase with the recombination rates when using 100 or more loci. On the other hand, the estimation of splitting times remained consistent as the number of loci increased. In the absence of recombination, the estimators of the IM model parameters remained consistent.