We studied sequence variation in the nuclear ribosomal internal transcribed spacers (ITS-1 and ITS-2) in 111 individuals from 11 populations/localities of the sponge Crambe crambe across the core species range in the western Mediterranean Sea and Atlantic Ocean. We report the first confirmed instance of intragenomic variation in sponges. Phylogeographical, nested clade and population genetic analyses were used to elucidate the species’ evolutionary history. The study revealed highly structured populations affected by restricted gene flow and isolation-by-distance. A contiguous range expansion in the whole distribution area of the sponge was inferred. Phylogenetic analyses indicate a recent origin of most sequence types that could be explained by a recent origin of the species or a by recent bottleneck event in the studied area. A recent expansion of the distribution range to the Macaronesian region from the Mediterranean Sea was also detected, suggesting that C. crambe was recently introduced from the Mediterranean Sea to the Atlantic Ocean via human-mediated transport, and that the pattern observed is not the result of a natural biogeographical relationship between these zones.