Fertilization in hermaphroditic urochordates requires efficient mechanisms to prevent self-mating. By comparing gonadal transcripts of three genetically unrelated Ciona intestinalis individuals by suppression subtractive hybridization (SSH), we have previously identified a highly polymorphic gene coding for a transmembrane receptor which is expressed in follicle cells surrounding the mature oocyte [Kürn U, Sommer F, Hemmrich G, Bosch TCG, Khalturin K. Allorecogmition in urochordates: identification of a highly variable complement receptor-like protein expressed in follicle cells of Ciona. Dev Comp Immunol 2007; 31(4): 360-71]. Here, we show that in addition to follicle cells, oocytes also express variable genes. We have identified four novel Ciona genes coding for zona pellucida (ZP) domain proteins which are expressed in developing oocytes and which significantly vary among individuals. ZP containing proteins are thought to play a crucial and conserved role in controlling fertilization. Our results provide strong evidence that in Ciona components of both follicle cells and oocytes show a high degree of interindividual variability and, therefore, may take part in the prevention of self-mating as well as in the maintenance of species-specific fertilization.