Alfalfa (Medicago sativa L.) is a major perennial forage legume crop with numerous nutritional and environmental benefits. This allogamous and autotetraploid species whose varieties are synthetic populations, has a highly polymorphic genome and a short linkage disequilibrium. Allele mining strategy on targeted candidate genes is an option to select valuable parents for breeding. In this paper, we assessed allelic diversity of CAD and WXP1 genes, involved in lignin biosynthesis and drought tolerance respectively, in a set of 384 individuals. For CAD which had two splice forms, 30 and 31 variants (out of 1077 and 906 base pairs of the coding sequences, respectively) have been observed including 37 and 52% of non-synonymous mutations. More variants were observed in WXP1 sequence, with 157 observed in WXP1 coding sequence (coding sequence of 1116 base pairs), including 60% non-synonymous mutations. Among the non-synonymous mutations, some probably affected protein function. Both genes were under purifying selection, especially CAD with dN/dS rate of 0.05 and 0.12 for both splice forms, against a rate of 0.26 for WXP1. Difference in variant proportion is probably explained by differential selective pressure that may be induced by contrasted expression levels. Indeed, CAD is highly and continually expressed whereas WXP1 is induced in some specific conditions. Further studies assessing the impact of variants on phenotype will help to conclude on the allele mining strategy in alfalfa breeding.