<p>The status of <i>Apis mellifera ruttneri,</i> an endemic honey bee of the Maltese islands, was uncertain after a series of devastating Varroa mite infestations followed by ill-conceived replacement programs. Morphometric analysis, which was the method originally used to identify this honey bee subspecies, was carried out using 33 different parameters<i>.</i> Thirty-two colonies exhibiting morphometric data that corresponded to those in the original description of <i>A. m. ruttneri</i> were identified (<i>p</i> > 0.99). In addition, the mitochondrial DNA region spanning the tRNA<sup>leu</sup>-Cox2 region from colonies bearing the morphometric data associated with <i>A. m. ruttneri</i> was amplified (77% showed the P<sub>0</sub>QQ structure). The data presented confirm morphometric similarity with <i>A. m. siciliana</i> and <i>A. m. intermissa</i>. We report the presence of A4, A8 and A9 haplotypes in <i>A. m. ruttneri</i> (83%; frequency 0.189, 0.081 and 0.486 respectively). European haplotypes belonging to the C1, C2 and M7 haplotypes were also recorded (17%; 0.135, 0.081, 0027). Recommendations for the conservation of this honey bee are proposed.</p
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