ABSTRACT: Botryllus schlosseri, a subtidal cosmopolitan tunicate species, is abundant in many rocky shores along the Mediterranean and other European seas. A highly polymorphic microsatellite locus (BS-811) elucidated Botryllus populationgenetics in 3 localities along the Israeli coast (at Shikmona, Caesarea and Michmoret, 12 to 36 km apart from each other, north to south, respectively) during 8 seasonal samplings (2 yr). Four other loci were studied only in the Michmoret population. Theanalysis on 1156 scorable colonies revealed a high number of alleles per locus (up to 15 to 38 alleles), unique alleles for each population (8 to 13 alleles per locus), high heterozygous deficiency, rapid seasonal changes in allele frequencies at allsites, and the existence of natural chimeric colonies. Locus BS-811, which was studied in all 3 localities, revealed 34 to 40 alleles per locality, and a total of 64 alleles, of which 48% were unique to one or other of the localities. Only 24 coloniesfrom the 1153 studied were heterozygous on this locus. These results are discussed together with recent outcomes from B. schlosseri populations sampled in New Zealand, the east and west coasts of the USA and the Adriatic Sea, Croatia.