In 1990, dolphin morbillivirus (DMV) killed thousands of striped dolphins in the Mediterranean. Subsequently, the prevalence of the infection declined in this species. In 2006-2008, the virus killed not only numerous striped dolphins but also long-finned pilot whales. All partial sequences of the phosphoprotein and nucleoprotein genes obtained thus far from different host species during the 2006-2008 outbreak show 100% identity, suggesting that a single virus was involved, and these sequences are nearly identical to the 1990 Spanish strain. Here our first objective was to determine the sequence identity between the morbillivirus from the 2006-2008 outbreak and the 1990 Spanish strain by sequencing more extensive genomic regions of strains from one pilot whale and one striped dolphin stranded in 2007. The second objective was to investigate the relationship between the 1990 and 2007 strains by constructing a phylogenetic tree based on the phosphoprotein gene to compare several Cetacean morbilliviruses, and another tree based on the nearly complete genomes of Mediterranean DMV. The third objective was to identify the most variable regions in the DMV genomes. Results showed that the two 2007 Spanish strains were 99.9% identical over 9050 bp and should be considered the same virus, and that this virus is 99.3-99.4% similar to the 1990 Spanish strain. The phylogenetic trees, together with the common geographical area for the two outbreaks, suggest that the 2007 DMV strains evolved from the 1990 DMV strain. Pilot whales do not seem to have been exposed or infected during the 1990-1992 epidemic, since these populations appeared to be immunologically naïve in 2006-2008. Our results suggest that the virus may have evolved in striped dolphin populations prior to the 2006-2008 outbreak, after which it entered the long-finned pilot whale, perhaps aided by an alanine to valine mutation in the N-terminal domain of the fusion protein.