Microsatellite markers which are believed to be biallelic and codominant have been found to behave as multiallelic in diploid species like Cajanus cajan L. Millsp. The dominant amplification of SSR markers has now been well accepted as null allele for the absence of the amplification in such plants. Moreover the use of molecular markers depends upon the trait under study of a species and its inheritance. Consideration of inheritance of resistance of biotic stresses like Fusarium wilt in pigeonpea as monogenic or oligogenic based upon the classified scoring system of trait under study and limited population/sample size and limted number of markers may be misguiding. Therefore, the given report will help the young researchers in dealing with the problems associted with the starting difficulties and also to dig into the problems faced during experimentaion and data analysis in general and in case of biotic stress resistance breeding invoving molecular markers in particular.