In mammals, downstream function of the nuclear progestin receptor (PGR) can be differentially regulated in each target tissue by altering the expression levels of PGR mRNA variants. Such PGR isoforms have also been identified in birds and reptiles, but not in non-amniote vertebrates. Based upon extensive phylogenetic, syntenic and functional analyses, here we show that higher orders of Teleostei retain a single pgr gene, and that four different pgr transcript variants of the extant gene are expressed in the ovary of an evolutionary advanced perciform teleost, the gilthead seabream (Sparus aurata). Three of the isoforms (pgr_tv2, pgr_tv3 and pgr_tv4) arise from alternative pre-mRNA splicing resulting in different N-terminally truncated receptors, whereas one isoform (pgr_tv1) is a deletion variant. Seabream wild-type Pgr shows the highest transactivational response to native euteleostean progestins, 17α,20β-dihydroxy-4-pregnen-3-one and 17α,20β,21-trihydroxy-4-pregnen-3-one, whereas the Pgr_tv3 and Pgr_tv4 isoforms independently regulate novel nuclear and cytosolic mechanisms of dominant-negative repression of Pgr-mediated transcription. In the seabream ovary, the wild-type Pgr protein is localized in oogonia, in the nuclei of primary (previtellogenic) oocytes, as well as in follicular (granulosa) cells and the oocyte cytoplasm of early and late vitellogenic ovarian follicles. Expression of wild-type pgr, pgr_tv3 and pgr_tv4 was the highest in seabream primary ovaries, while expression of both inhibitory receptor isoforms, but not of pgr, decreased during vitellogenesis. Stimulation of primary ovarian explants in vitro with recombinant piscine follicle-stimulating hormone and estrogen differentially regulated the temporal expression of pgr, pgr_tv3 and pgr_tv4. These findings suggest that, as in mammals, ovarian progestin responsiveness in the seabream, particularly during early oogenesis, may be regulated through alternative splicing of the nuclear pgr mRNA. Thus, the dominant-negative mechanism of PGR transcriptional regulation likely evolved prior to the separation of Actinopterygii (ray-finned fishes) from Sarcopterygii (lobe-finned fishes).