| Summary: | <i>Streptocarpus ionanthus</i> (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of <i>Str. ionanthus</i> is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within <i>Str. ionanthus</i> using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of <i>Str. ionanthus</i>, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (<i>psb</i>M, <i>rps</i>3, <i>atp</i>F<i>-atp</i>H, <i>psb</i>C<i>-psb</i>Z and <i>psa</i>A<i>-ycf</i>3) and five genes with a high number of polymorphic sites (<i>rps</i>16, <i>rpo</i>C2, <i>rpo</i>B, <i>ycf</i>1 and <i>ndh</i>A) which could be investigated further for phylogenetic utility in <i>Str. ionanthus.</i> Phylogenomic analyses here exhibit low polymorphism within <i>Str. ionanthus</i> and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of <i>Str. ionanthus</i> phylogenetic relationships.
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