The sugarcane Breeding Unit in the National Agricultural Research Center for Kyushu Okinawa Region has been working on intergeneric hybridization between sugarcane (Saccharum spp. hybrid) and Erianthus (Erianthus arundinaceus) to develop innovative breeding materials. In the present study, we applied Erianthus-specific EaCIR1 and 5S rDNA markers to identify hybrids. EaCIR1 is a tandemly-repeated DNA sequence in the subtelomeric regions of most Erianthus chromosomes. Progenies produced by intergeneric crossing (sugarcane x Erianthus) were divided into three groups : group A had both EaCIR1 and 5S rDNA markers, group B had only the EaCIR1 marker, and the other group did not have either marker. Seedlings of group A exhibited poor growth and had intermediate DNA amounts between their parents. One of them lost dewlaps (joint part of leaf blade and sheath) as morphologically similar to Erianthus. These results indicated that group A was composed of intergeneric hybrids. Group B had dewlaps and growth characteristics similar to sugarcane instead of Erianthus. The amount of DNA in seedlings of group B was almost the same as that of their maternal sugarcane. Marker analyses with 28 Erianthus-specific primers revealed no Erianthus-specific band pattern in group B. These results did not present any evidence that Erianthus chromosomes were introduced into individuals of group B. Consequently, the EaCIR1 marker should not be Erianthus-specific. Additionally, we used marker analyses to investigate a large number of progenies produced by intergeneric crossing, and did not find any individuals that contained Erianthus chromosomes. This suggested that partial introduction of Erianthus chromosomes into progeny by intergeneric crossing was less likely.