Premise: The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sample yielded Mesozoic median ages.

Methods: We investigated node ages in Isoetes using two genomic datasets (plastome and nuclear ribosomal cistron) analyzed using three different clock models implemented in MrBayes (ILN, WN and TK02 models) and a conservative approach to calibration.

Key results: While topological results are consistently resolved in Isoetes, estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on datatype and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome dataset also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent recently established sister species Isoetes wormaldii to the dataset approximately doubled the average median node depth to the Isoetes crown group.

Conclusions: There is no consistent support for a Cenozoic origin of the living clade Isoetes. We obtained seemingly well-founded, yet strongly deviating results, depending on datatype and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.