Study of the DNA repair and genome stability in plants is directly dependent on the availability of an easy, inexpensive, and reliable assay. Marker gene-based homologous recombination (HR) assays were introduced more than a decade ago and have been intensively used ever since. Here, we compared several transgenic Arabidopsis and tobacco lines that carried in their genome the luciferase (LUC) or the beta-glucoronidase (uidA or GUS) substrates for HR. The average recombination frequency detected with the luciferase transgene was nearly 9.0-fold higher in Arabidopsis and 12.4-fold higher in tobacco plants. Importantly, both transgenes were under the control of 35S promoter and had similar expression levels throughout the plants. Irradiation with UVC increased the HR frequency similarly in both transgenes. The actual difference in the frequency of HR in Arabidopsis and tobacco possibly results from differing sensitivity to detection of transgene activity. Thus, we could suggest that luciferase recombination assay, due to its higher sensitivity, should be the assay of choice when plant genome stability is studied.