Randomly amplified polymorphic DNA (RAPD) markers quickly provide linkage information, especially in conifers where haploid megagametophytes can be used for genotyping. Traditionally use of slab gel electrophresis results in qualitative data that can be manually manipulated to gain semiquantitative information about the polymorphic RAPD fragments. We have proposed the use of an integrated microfluidic chip-based system as a new tool in the analysis of polymorphic RAPD fragments. The chip-based method was found to be very sensitive,requiring much less sample and only quarter the time compared to the agarose gel method. The automated data analysis sizes and quantitates the DNA fragments, thus yielding a more thorough,reproducible, sensitive, and rapid analysis.