Eucommia ulmoides Oliv. is a dioecious species. Currently, there is no method to identify the sex during the juvenile stage that lasts a relatively long time. This study aimed to develop a sex specific Amplified Fragment Length Polymorphism (AFLP) marker for Eucommia ulmoides Oliv. Of a total of 64 AFLP primer combinations screened, primer combination E-ACA/M-CTT produced a 350 bp male-specific marker. This 350 bp AFLP marker was converted into a 247 bp Sequence Characterized Amplified Region (SCAR) marker. Results suggest that the SCAR marker can be utilized for early sexual identification in Eucommia ulmoides Oliv., and it will greatly facilitate future breeding programs.