The genus Medicago (Leguminosae, Papilionoideae) contains about 90 species including the important forage crop alfalfa Medicago sativa and the genomic model Medicago truncatula. Despite intensive research on the genus because of its agricultural importance, there is a relative lack of information about chromosome number and genome size in some Medicago species, especially those from Medicago section Buceras that were formerly placed in the sister genus Trigonella, and are paraphyletic to the remainder of the genus Medicago. Past studies revealed that previous species delimitations did not conform well with complex patterns of morphological or genetic variation. Some published chromosome numbers, e.g. 2n = 28 and 2n = 44, differ from those of the rest of the genus, which are mostly 2n = 16 or polyploids thereof, although some cases of aneuploid reduction or dysploidy (e.g. 2n = 14) do exist. Here we estimated phylogenetic relationships of 42 accessions corresponding to 14 currently recognized Medicago species that are paraphyletic to the remainder of Medicago with a focus on Medicago monantha; for a number of those accessions we obtained estimates of genome size (39) and chromosome number (14). We can confirm the delimitation of two species within M. section Buceras and our data suggest that there are at least two entities with distinct geographic distributions within the currently recognized species M. monantha, which differ in chromosome number and genome size. Our data also suggest that polyploidy and post-polyploid descending dysploidy played a significant role in genome evolution within M. section Buceras. Our data provide a strong foundation for whole-genome sequencing projects and further in-depth research of these paraphyletic lineages.