Two PCR-based techniques, RAPD (Randomly Amplified Polymorphic DNA) and ISSR (Inter-Simple Sequence Repeat), were used for analysis of somaclonal variation in almond shoots regenerated from in vitro cultures. No polymorphic band classes were generated when analysing 20 axillary branching regenerated shoots with 64 RAPD and 10 ISSR primers. This result allowed us to use these shoots (mother-plants) as internal controls when analysing somaclonal variation associated with shoots recovered from adventitious regeneration, meristem culture protocols, virus elimination programs and genetic engineering. No polymorphic bands were generated when 15 randomly chosen shoots, regenerated from the previously mentioned techniques, were tested with 10 ISSR and 40 (of the previous 64) RAPD primers. These results allow us to conclude that the studied regenerants possess high genetic stability and that the protocols used seem to be suitable for maintaining the integrity of the genome.