The mutation detections of KRAS and BRAF genes are of significant importance to predict the responses to anti-cancer therapy and develop new drugs. In this paper, we developed a multi-step fluorescence resonance energy transfer (FRET) assay for multiplex detection of KRAS and BRAF mutations using cationic conjugated polymers (CCP). The newly established detection system could detect as low as 2% mutant DNAs in DNA admixtures. By triggering the emission intensity change of CCP and the dyes labeled in the DNA, four possible statuses (three mutations and one wildtype) can be differentiated in one extension reaction. The detection efficiency of this new method in clinical molecular diagnosis was validated by determining KRAS and BRAF mutations of 51 formalin-fixed paraffin-embedded (FFPE) ovary tissue samples. Furthermore, the result of the CCP-based multi-step FRET assay can be directly visualized under UV light so that no expensive instruments and technical expertise are needed. Thus, the assay provides a sensitive, reliable, cost-effective and simple method for the detection of disease-related gene mutations. In the era of personalized medicine, understanding the mutation profile of individual tumors is useful for conducting anti-cancer therapy. In the past few years, mutations in KRAS and BRAF genes have been discovered in many different human cancers [1,2]. Mutation detection in these genes has shown good results in predicting response to anti-EGFR therapy in patients with metastatic colorectal cancer (CRC) [3][4][5][6]. Studies are underway to figure out the roles of KRAS and BRAF mutations as predictive biomarkers and drug targets in other cancers therapy [2,[7][8][9]. Therefore, it is of significant importance to develop effective techniques for the detection of KRAS and BRAF mutations that can predict the response to cancer therapy as well as develop new drugs. Currently, various methods for KRAS and BRAF mutation detection have been reported, such as single strand conformation polymorphism analysis (SSCP) [10], highresolution melting analysis (HRMA) [11], direct sequencing [10,12], real-time quantitative-PCR (RQ-PCR) method [13][14][15], and SNaPshot assay [16,17]. SSCP and HRMA are pre-screening approaches that demand subsequent sequence verification of potential mutations, leading to the increased time and cost. Direct sequencing is expensive and not sensitive enough to detect low abundant mutations. RQ-PCR has much higher analytical sensitivity for mutation detection. However, the utilization of organic dyes-labeled oligonucleotide probes carries a high cost. Compared to direct sequencing and RQ-PCR methods, SNaPshot assay can simultaneously screen several mutations and reduce the cost of assays. Nevertheless, this method still requires expensive instruments and technical expertise. Thus, a simple, inexpensive, sensitive, and multiplex mutation diagnosis method remains to be explored.