The main forage legume species (alfalfa, red clover, white clover) belong to the same clade than the model species Medicago truncatula whose genome has been sequenced. Attempts for sequencing forage legume crops, even if they are heterozygous and may be polyploid, are also reported. In addition to sequence information, new methods of genotyping are being developed. These methodologies offer new possibilities to conduct genetic analysis of traits of agronomic interest. The traits can be studied in model species, with QTL or genome-wide association studies that end to the identification of candidate genes. The genetic studies can also be carried out in the crop species, with analysis of genetic diversity and structure, QTL studies, association studies based on a candidate gene or a genome-wide approach, bulk-segregant analysis or genomic selection in a near future. The new possibilities of high throughput genotyping increase the power of these studies. It is expected that breeding program on forage legumes will benefit from these studies.