BACKGROUND: Alfalfa (Medicago sativa) is one of the most valuable forages in the world. As an outcrossing species, it needs bright flowers to attract pollinators to deal with self-incompatibility. Although various flower colors have been observed and described in alfalfa a long time ago, the biochemical and molecular mechanism of its color formation is still unclear. METHODS: By analyzing alfalfa lines with five contrasting flower colors including white (cream-colored), yellow, lavender (purple), dark purple and dark blue, various kinds and lev...