A new, well-preserved mysticete fossil is described and diagnosed here as Joumocetus shimizui, gen. et sp. nov. The holotype specimen was recovered from the earliest Late Miocene, Haraichi Formation, Annaka Group, Gunma Prefecture, Japan. Although many cetotheres have been found from the Pacific realm, the Cetotheriidae sensu stricto is relatively rare in terms of taxonomic diversity and also abundance of specimens. Joumocetus will be the fourth genus of the Cetotheriidae sensu stricto from the Pacific and the geologically earliest and most archaic Cetotheriidae sensu stricto yet reported. Joumocetus retains a number of primitive characteristics, and our phylogenetic analysis indicates that Joumocetus is placed basally among the Cetotheriidae sensu stricto. Our analysis clearly indicates a monophyly of the Cetotheriidae sensu stricto and of a clade that consists of Balaenopteridae, Eschrichtiidae, and cetotheres. The results also indicate the monophyly of the following two groups: cetotheres not belong to Cetotheriidae sensu stricto (= Isanacetus-group) and Cetotheriidae sensu lato (= Isanacetus-group Cetotheriidae sensu stricto); however, the monophylies of these groups are not well supported by bootstrap analysis. Consequently, the relationships and definition of these mysticete taxa remain unclear. Based on the present study and a review of previous studies, we suggest that the Isanacetus-group is a paraphyletic taxon that includes the ancestors of two clades, Balaenopteridae Eschrichtiidae and the Cetotheriidae sensu stricto.