Orthology relations can be used to transfer annotations from one gene (or protein) toanother. Hence, detecting orthology relations has become an important task in the post-genomicera. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneousassignment of orthology relations. In closely-related species, gene neighborhood information can beused to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a softwarefor accurately predicting pairwise orthology relations based on gene neighborhood conservation.Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthologydetection, OrthoGNC can be employed to investigate the conservation of genomic contextamong potential orthologs detected by other methods. OrthoGNC is freely available online athttp://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.