Recombination is well known as a complicating factor in the interpretation of molecular phylogenies. Here we describe a maximum likelihood sliding window method based on a likelihood ratio test for scanning DNA sequence alignments for regions of incongruent phylogenetic signals, such as those influenced by recombination. Using this method, we identify several instances of gene conversion between paralogous chaperonin genes in euryarchaeote Archaea, many of which are not detected by two other widely used methods. In the Thermococcus/Pyrococcus lineage, where a gene duplication producing a and b paralogues predates the divergence of Thermococcus strains KS-1 and KS-8, gene conversion has homogenized portions of the a and b genes in KS-8 since the divergence of these two strains. A region near the 3' end of the a and b paralogues in the methanogen Methanobacterium thermoautotrophicum also appears to have undergone gene conversion. We apply the method to two additional test data sets, the argF gene of Neisseria and a set of actin paralogues in maize, and show that it successfully identifies all the recombinant regions that were previously detected with other methods. Our approach is relatively insensitive to the presence of divergent sequences in the alignment, making it ideal for detecting recombination between both closely and distantly related genes.