This paper presents investigations of segregation distortion of six rice F2 populations generated from reciprocal F1 hybrids grown at three locations varied at altitudes from 400 to 2200 m. The F1s were derived from reciprocal crosses between cv. XMG, which is a japonica landrace traditionally grown at 2650 m altitude, and cv. N34, which is a japonica restorer possessing a fertility restoring (Rf) gene and cytoplasm of male sterility (CMS) donated by an indica cultivar. Among nine morphological traits of the F2 populations, only one was in normal distribution, eight were distorted in all or at least one population. Out of 16 polymorphic PCR markers, 10 markers distributed on 7 chromosomes were significantly distorted. Among these markers, RMAN7 and RM257 were distorted in both of the reciprocal populations, which suggested that nuclear genes had strong effects on segregation distortion. The other makers were distorted only in the populations with cytoplasm donated by XMG or N34. The results indicated that segregation of DNA markers was affected by cytoplasm background. Segregation distribution was also affected by altitude, since segregation distortions of most of the markers were detected not in all the three populations generated from F1 grown at the three altitudes, but only in one population from F1 grown at one altitude. Marker M45461, which is located within Rf-1 locus, was severely distorted towards N34 in all the populations with cytoplasm donated by N34, but not in the populations with cytoplasm provided by XMG. The results indicated that interaction between CMS and Rf gene had strong effects on distortion. Results of this study indicated that japonica cytoplasm did not cause distortion favouring a special parent, but indica cytoplasm made distortion favouring a maternal parent. The results suggested that indica cytoplasm was not well compatible with japonica nuclear background, while japonica cytoplasm did not have such trouble with indica nuclei. This study also found that the six F2 populations were divergent into two groups due to difference of cytoplasm background.