The aim of this note is to overview the characteristics of the Phylogenetic Diversity (PD) method in order to quantify genetic diversity in animal genetic resources conservation programs. The PD method performance has been compared with that of the Weitzman approach on a dataset consisting in 398 individuals belonging to 11 Spanish sheep breeds that were genotyped for a set of 14 microsatellites. Results from the PD and the Weitzman methods are similar. However, the PD method is less computing intensive thus allowing for its use at individual level. Moreover the PD does not need the assumption of ultrametricity of the distances. The use of the PD method in livestock conservation programs can be advanteageous with respect the Weitzman approach.