Ratio of functional changes from orthologous genes is being widely used for detecting the signature for natural selection between species. However, one to one orthologous genes allows only for the analysis due to methodological limitation. A number of genes have in-paralogs as a result of gene expansion in crops. Here, we report a new approach for detecting accelerated evolution, which includes in-paralogs as well as one to one orthologs. This new approach can detect many novel accelerated genes among rice in-paralogs, which have not been investigated yet.