The sequencing and comparison of complete plastid genomes is becoming a standard method in plant phylogenomics, and many researchers have used this approach to generate hypotheses on plant phylogenetic relationships over the past decade. Due to the widespread availability of next-generation sequencing, complete plastid genome sequences are currently being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly and annotation are needed, as both processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing and characterizing three complete plastid genomes of the aquatic plant genus Cabomba. We accompany our findings by a detailed description of the bioinformatic workflow employed for assembling and annotating the plastid genome sequences. Importantly, we share a total of seven software scripts for plastid genome assembly and annotation as well as for generating assembly quality statistics, enabling other researchers to evaluate and replicate our bioinformatic analyses step by step. The results of our sequencing efforts illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content.