Abstract: The inheritance regularity of wild specific loci for Erianthus arundinacius and Saccharum spontaneum L. from intergeneric hybrid complex (E. arundinaceus × S. spontaneum) inheriting to generations was investigated, in order to provide theoretical basis for exploring new sugarcane parents. AFLP-PCR molecular markers combined with capillary electrophoresis were used to analyze the transmission dynamics of wild specific loci over generations and also clarify the genetic relationship among these materials. A total of 3695 loci were amplified from 29 AFLP primer combinations, with a polymorphic ratio of 97.89%. The genetic fragments derived from E. arundinacius and S. spontaneum were 43.96% and 56.04% respectively. The average heritability of E. arundinacius in F1, BC1 and BC2 were 8.25%, 1.9% and 0.63%, respectively, and the average heritability of S. spontaneum in F1, BC1 and BC2 was 16.98%, 2.4% and 0.21% respectively. Both indicated a reduction of foreign specific genetic loci over generations. By analyzing the ratios of sugarcane specific loci that remained in different generations, the genetic information of GT02-761 has been ranked first in F1. The average percentage of special loci for GT05-2743 inheriting to BC1 was 92.75%. The heritability for ROC23 inheriting to BC2 was the lowest, and the heritability for FN39 was the highest, up to 94.32%.The cluster analysis showed that the intergeneric hybrid complex was inherited more from male parent and the progeny from the intergeneric hybrid complex were inherited more from the sugarcane (Saccharum spp.), which was consistent with the analysis of molecular genetic relationship. The results showed that the genetic loci for the hybrids from intergeneric hybrid complex had changed a lot compared with that of intergeneric hybrid complex in the process of genetic recombination for three generations. Thus, this work analyzed the inheritance regularity for two parents inheriting to three generations, and the outcome might provide suggestions for future breeding.