Common (bread) wheat is an allohexaploid species (Triticum aestivum L.) with 3 compensating genomes AABBDD (2n=6x=42 chromosomes). Traditionally genetic and physical mapping in this most important cereal crop has been based on molecular markers (RFLPs, PCR, Insitu hybridization etc). The recent development in producing deletion lines of common wheat (using Aegilops cylindricum genome) has revolutionized the physical mapping of wheat chromosomes. During present study, deletion lines of chromosomes 5A of common wheat were used to identify RAPD (Randomly Amplified Polymorphic DNA) based molecular markers specific for short and/or long arm of chromosome 5A. Out of the 7 RAPD primers used, OPA-07 showed useful polymorphism for long arm deletion lines viz; del5AL-10 and del5AL-23. By comparing the C-banding karyotype of the deletion lines, it is inferred that the primer (OPA-07) anneals to the distal half of the long arm of chromosome 5A.