Objective: The self cross colonial prochordate, Botryllus schlosseri ( B.schlosseri ) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B. schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods: AFLP markers are extremely sensitive to even small sequence variation, using PCR and high resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each primer combination generated from 80 to more than 120 bands, of which average 25.85% polymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2, F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation new loci and lost loci among F1, F2, F3 and F4 were observed. These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southern hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion: These results suggest that there are high frequency of polymorphic loci and mutation in genome of B. schlosseri. Gene deletion or low diversity may be the reason for high rate of death of the offspring of inbred laboratory reared strains. Objective: The self cross colonial prochordate, Botryllus schlosseri (B.schlosseri) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B. schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods: AFLP markers are extremely sensitive to even small sequence variation, PCR and high resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each The primer combination generated from 80 to more than 120 bands, of which average 25.85% polymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2, F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation new loci and lo These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southern hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion: These special fragments were cloned and sequenced. results suggest that there are high frequency of polymorphic loci and mutation in genome of B. schlosseri. Gene deletion or low diversity may be the reason for high rate of death of the offspring of inbred laboratory reared.