Summary Combined use of two newly designed PCR primers with already described rpl2 and trnH primers, yields amplification of three non-independent products from the hypervariable JLA region of eucalypt chloroplast. Polymorphism analysis of the resulting PCR markers is proved to be a time- and cost-efficient alternative to traditional cpDNA techniques as RFLP or sequencing for Eucalyptus globulus Labill. population genetics studies.