Chromosomal structural rearrangement in Paeonia brownii and P. californica (2n = 10) was studied by in situ hybridization using 18S rDNA probes. Six major rDNA sites were detected in mitotic cells of P. californica; six major and two minor rDNA sites were found in P. brownii. Two cytotypes (A and B), with different chromosomal morphology and (or) rDNA locations, were observed in the population of P. californica. Cytotype A, with rDNA sites only on the short arms of chromosomes, was considered to be the normal cytotype. Both translocation and pericentric inversion may have occurred to give rise to cytotype B, in which one homolog of chromosome 4 has rDNA sites on both arms while its homolog has no rDNA sites: one homolog of chromosome 3 has a rDNA site on the long arm. Two rearranged cytotypes, C and D, were observed in the population of P. brownii. Given that the normal cytotype of P. brownii is most likely to have six major rDNA sites on the short arms of chromosomes 3, 4, and 5, and two minor sites on the short arms of chromosome 2, cytotype C may have resulted from a translocation between the short arm of one homolog of chromosome 2 and the long arm of one homolog of chromosome 4, and cytotype D may have resulted from a translocation between the short arm of one homolog of chromosome 3 and the long arm of one homolog of chromosome 4. These results supported previous observations, based on meiotic configurations, that chromosomal structural rearrangement occurred frequently in P. brownii and P. californica.