We constructed a physical map of O. sativa ssp. japonica cv. ZH11 and compared it and its random sample sequences with the Nipponbare RefSeq derived from the same subspecies. This comparison showed that the two japonica genomes were highly syntenic but revealed substantial differences in terms of structural variations, rates of substitutions and indels, and transposable element content. For example, contractions/expansions as large as 450 kb and repeat sequences that were present in high copy numbers only in ZH11 were detected. In tri-alignment regions using the indica variety 93-11 sequence as an outgroup, we found that: (1) the substitution rates of the two japonica-indica inter-subspecies comparison combinations were close but almost a magnitude higher than the substitution rate between the japonica rice varieties ZH11 and Nipponbare; (2) of the substitutions found between ZH11 and Nipponbare, 47.2% occurred in ZH11 and 52.6% in Nipponbare; (3) of the indels found between ZH11 and Nipponbare, the indels that occurred in ZH11 were 15.8 times of those in Nipponbare. Of the indels that occurred in ZH11, 75.67% were insertions and 24.33% deletions. Of the indels that occurred in Nipponbare, 48.23% were insertions and 51.77% were deletions. The ZH11 comparative map covered four Nipponbare physical gaps, detected assembly errors in the Nipponbare sequence, and was integrated with the FSTs of a large ZH11 T-DNA insertion mutant library. ZH11 BAC clones can be browsed, searched, and obtained at our website, http://GResource.hzau.edu.cn.