The endemic subspecies of the southern grey shrike Lanius meridionalis koenigi in the Canary Islands is restricted to four islands (Tenerife, Gran Canaria, Fuerteventura and Lanzarote) and two islets (Alegranza and La Graciosa). A total of 174 shrikes was captured from these areas. In the Control Region of the mtDNA, 56.3% of the birds presented two tandem repeats, 31.6% three, 10.4% 2+3 repeats and finally 1.7% 2+3+4 tandem repeats. The frequency of tandem repeats was significantly different among the shrike populations analysed. The greatest genetic diversity, in relation to the tandem repeats, appeared on Fuerteventura. The proportion of tandem repeats in L. m. koenigi from the Canary Islands was clearly different in relation to the L. m. meridionalis from the Iberian Peninsula.