Here, scientists from 19 European countries, most of them collaborating in Working Group 4: "Diversity and Vitality" of COST Action FA 0803 "Prevention of honey bee COlony LOSSes" (COLOSS), review the methodology applied in each country for discriminating between honey bee populations. Morphometric analyses (classical and geometric) and different molecular markers have been applied. Even if the approach has been similar, however, different methodologies regarding measurements, landmarks or molecular markers may have been used, as well as different statistical procedures. There is therefore the necessity to establish common methods in all countries in order to have results that can be directly compared. This is one of the goals of WG4 of the COLOSS project.