A family of seven allelic genes encoding self/nonself signal proteins (pheromones) in the polar (cold-adapted) marine hypotrichous ciliate, Euplotes nobilii, were cloned from the somatic sub-chromosomic genome of the cell macronucleus. The determination of their full-length nucleotide sequences shows that their open reading frames specify proteins of 83 to 94 amino acid residues which represent the cytoplasmic pheromone precursors (pre-pro-pheromones). Two proteolytic steps would thus remove the pre and pro segments formed by tightly conserved sequences, before the secretion of the structurally more variable mature proteins. At odds with respect to the general structural organization of the macronuclear genes of the hypotrichous ciliates, the 5’ region of all the cloned pheromone genes is significantly longer than the respective coding region (approximately, 350 versus 250 nucleotides). Considered jointly with the tight sequence conservation, this feature implies that the 5’ region is site of specific activities in the mechanism of pheromone gene expression.