The quillwort Isoetes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (N_e) is expected for narrow endemic species (NES). Here, we evaluated genetic diversity, population structure, and N_e of I. cangae to provide information for conservation programs. Conservation biology studies centered in a single‐species show some limitations but they are still useful considering the limited time and resources available for the protection of species at risk of extinction. Our analyses were based on 55 individuals collected from the Amendoim lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and effective population size (N_e) in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential, all individuals should be treated as one demographic unit.

Here, we provide:

- Draft genome for Isoetes cangae: and their raw data in .tar.gz and contigs alignment in .fasta.

- R scripts for all analyses, and they are also available on: https://github.com/jdalapicolla/Isoetes_Scripts.R

- Raw VCF and Filtered VCF files in .7z

- Supplementary Information in .pdf