Premise: Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. RADseq has been a popular sequencing technique for the reconstruction of hybridization in the Next Generation Sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization but the specific hybrid origins of taxa have not been yet clarified. Methods: We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with datasets that include several species and complex hybridization patterns. Results: Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while less clear signals were observed for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata and M. sativa. Conclusions: Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when most divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.