Identifying synapomorphic morphological characters is needed to select and then accurately place fossils as calibrations on a phylogeny in molecular-dating analyses. The plant family Myrtaceae, with 130 genera and 5500 species, has nine different pollen types, whereas the fossil pollen record of Myrtaceae, represented by the genus Myrtaceidites, putatively extends back to the Cretaceous and also contains at least nine distinct morphospecies. To reveal potential links between extant and fossil pollen, we optimised pollen characters scored from a recent family-wide review of extant Myrtaceae pollen using scanning electron microscopy (SEM) onto a phylogeny of 111 taxa inferred from two chloroplast (matK and ndhF) and one nuclear (internal transcribed spacer, ITS) loci. Our findings indicate the potential use of colpus morphology in diagnosing pollen types in Myrtaceae, whereas the majority of character states of exine pattern, presence of apocolpial island and pollen width appear to be homoplasious. The results of the present study have implications for understanding the relationship between fossil morphospecies and extant Myrtaceae species, and their reliable choice in molecular dating.