Cytoplasmic male sterility (CMS) breeding systems expedite the production of hybrid seed in many crops. By taking advantage of an interaction between the nucleus and the cytoplasm that regulates the production of viable pollen, CMS eliminates the need for manual emasculation. Markers that can identify the status of cytoplasmic male sterility and nuclear restorer-of-fertility (Rf) genes are valuable for identification and development of CMS systems. In chile pepper (Capsicum annuum), reliable markers for the Rf trait have been elusive. To identify viable Rf markers for chile pepper, markers were created using identified Rf candidate genes and compared them to the most effective previously reported Rf markers. The previously reported cleaved amplified polymorphic sequence (CAPS) marker Co1Mod1-CAPS and PPR-derived CaRf648, had the highest rates of correctly predicting the Rf phenotype for an F2 segregating population. The Co1Mod1-CAPS marker detected the Rf genotype, and CaRf648 quickly and inexpensively identified Rf presence.