BackgroundBalanophoraceae plastomes are known for their highly condensed and re-arranged nature alongside the most extreme nucleotide compositional bias known to date, culminating in two independent reconfigurations of their genetic code. Currently, a large portion of the Balanophoraceae diversity remains unexplored, hindering, among others, evolutionary pattern recognition. Here, we explored newly sequenced plastomes ofSarcophyte sanguineaandThonningia sanguinea. The reconstructed plastomes were analyzed using various methods of comparative genomics based on a representative taxon sampling.ResultsSarcophyte,recovered sister to the other sampled Balanophoraceae s. str., has plastomes up to 50% larger than those currently published. Its gene set contains five genes lost in any other species, includingmatK. Fivecis-spliced introns are maintained. In contrast, theThonningiaplastome is similarly reduced to published Balanophoraceae and retains only a singlecis-spliced intron. Its protein-coding genes show a more biased codon usage compared toSarcophyte,with an accumulation of in-frame TAG stop codons.Structural plastome comparison revealed multiple, previously unknown, structural rearrangements within Balanophoraceae.ConclusionsFor the “minimal plastomes” ofThonningia, we propose a genetic code change identical to sister genusBalanophora.Sarcophytehowever differs drastically from our current understanding on Balanophoraceae plastomes. With a less-extreme nucleotide composition, there is no evidence for an altered genetic code. Using comparative genomics, we identified a hotspot for plastome reconfiguration in Balanophoraceae. Based on previously published and newly identified structural reconfigurations, we propose an updated model of evolutionary plastome trajectories for Balanophoraceae, illustrating a much greater plastome diversity than previously known.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09422-1.