<i>Spiraea prunifolia</i> f. <i>simpliciflora</i> Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of <i>S. prunifolia</i> f. <i>simpliciflora</i>, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus <i>Spiraea</i> was monophyletic and sister to the clade of <i>Sibiraea angustata</i>, <i>Petrophytum caespitosum</i> and <i>Kelseya uniflora</i>. Within the genus <i>Spiraea</i>, the sections <i>Calospira</i> and <i>Spiraea</i> were monophyletic, but the sect. <i>Glomerati</i> was nested within the sect. <i>Chamaedryon</i>. In the sect. <i>Glomerati</i>, <i>S. prunifolia</i> f. <i>simpliciflora</i> formed a subclade with <i>S. media</i>, and the subclade was sister to <i>S. thunbergii</i> and <i>S. mongolica</i>. The close relationship between <i>S. prunifolia</i> f. <i>simpliciflora</i> and <i>S. media</i> was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus <i>Spiraea</i>. The newly reported complete plastome and nrDNA transcription unit sequences of <i>S. prunifolia</i> f. <i>simpliciflora</i> provide useful information for further phylogenetic and evolutionary studies of the genus <i>Spiraea</i>, as well as the family Rosaceae.