Largely shallow and putatively explosive divergences in the family Leporidae (rabbits and hares; order: Lagomorpha) have resulted in phylogenetic relationships that remain currently unresolved. These rapid radiations in different branches of the leporid tree have resulted in conflicting phylogenetic hypotheses. However, this phylogenetic incongruence may also result from inadequate taxon or character sampling, due to the high number of extinct and difficult to sample extant species, and highly conserved morphological characters. Sylvilagus (cottontail rabbits) constitute about 30% of the known extant leporid species. New species are routinely being recognized, and phylogenetic relationships with respect to other leporid genera, and within the genus, have failed to be recovered with certainty. Within Sylvilagus, the South American S. brasiliensis is the most widespread and poorly known taxon, likely comprising multiple species. Here, we reanalyze previously published molecular data from phylogenetic studies on Leporidae, focusing on the S. brasiliensis group, and assessing phylogenetic relationships using bifurcating trees and split networks to identify phylogenetic regions with polytomies. We estimate differentiation and phylogenetic relationships of molecular lineages within the S. brasiliensis group. Our analyses suggest that this group contains a number of divergent taxa, well differentiated from other cottontail species. We discern two major polytomies during leporid diversification. The first, at the base of the leporid radiation, likely resulted from a combination of hard (rapid radiation) and soft polytomies (high number of unsampled extinct species). The second polytomy likely resulted from a rapid radiation during the initial diversification of the genus Sylvilagus. We conclude that only a molecular phylogeny based on a broader taxonomic representation will fully resolve leporid phylogeny.