The reduction of chromosome number in plant somatic cells is a rare phenomenon. In this study, the tetraploid scion, chimeric scion, and diploid rootstock of the same wild germplasm of Hevea brasiliensis were used to analyze the position effect of tetraploid cell proportion in chimeras by flow cytometry, and the origins of tetraploid and chimeric identified by SSR markers. The results showed that the proportion of tetraploid cells in the chimera plants decreased to 65.58% in the seventh leaf layer from 80.50% in the first leaf layer. The 32 bands amplified by 18 pairs of primers were identical in the tetraploid and chimera, and there were 28 different bands compared with 28 bands of the diploid rootstock, indicating that the chimera was derived from the spontaneous somatic ploidy reduction of tetraploid. The peak ratio of two alleles in one of the 18 loci was 3:1, indicating that the tetraploid germplasm was not an autotetraploid produced by chromosome doubling of somatic cells, but an allotetraploid derived from sexual polyploidization of the 2n egg and 2n pollen. This study discovered and proved the phenomenon of ploidy reduction of an allotetraploid in Hevea brasiliensis.