Understanding linkage block size and molecular mechanisms of recombination suppression is important for plant breeding. Previously large linkage blocks ranging from 14 megabases to 27 megabases were observed around the rice blast resistance gene Pi-ta in rice cultivars and backcross progeny involving an indica and japonica cross. In the present study, the same linkage block was further examined in 456 random recombinant individuals of rice involving 5 crosses ranging from F(2) to F(10) generation, with and without Pi-ta containing genomic indica regions with both indica and japonica germplasm. Simple sequence repeat markers spanning the entire chromosome 12 were used to detect recombination break points and to delimit physical size of linkage blocks. Large linkage blocks ranging from 4.1 megabases to 10 megabases were predicted from recombinant individuals involving genomic regions of indica and japonica. However, a significantly reduced block from less than 800 kb to 2.1megabases was identified from crosses of indica with indica rice regardless of the existence of Pi-ta. These findings suggest that crosses of indica and japonica rice have significant recombination suppression near the centromere on chromosome 12.