Sensitivity of alfalfa to acidity and aluminium (Al) toxicity in soil is the major limiting factor in broadening of its growing area. Due to lack of Al tolerance in primary alfalfa germplasm, there is a need for transfer of genes for Al tolerance from other Medicago germplasm. One of the identified sources of Al tolerance is M. sativa ssp. caerulea accession PI 464724, which was used as a female parent in our study. The objectives of this study were: (i) obtaining the tetraploid offspring from 2x–4x M. sativa ssp. caerulea – M. sativa ssp. sativa spontaneous crosses, and (ii) development of a breeding strategy for Al/acid tolerance in alfalfa, using M. sativa ssp. caerulea as a source of Al tolerance. Out of eleven fully developed plants, five were morphologically similar to M. sativa ssp. caerulae, while six plants were similar to M. sativa ssp. sativa. All tested plants were fertile, with the pollen viability ranging from 21.45 to 97.09% and the average number of ovules per plant from 8.80 to 12.29. Eleven SSR primer pairs confirmed the hybrid nature of M. sativa ssp. caerulae × M. sativa ssp. sativa offspring. Both the Cluster Analysis and the Principal Coordinates Analysis separated plants in the caerulae type from plants in the sativa type, with one exception. Strategies based on conventional and molecular marker breeding efforts could lead towards development of tolerant alfalfa cultivars and successful crop production on acidic, Al-contaminated soils.