Leaf cuticle micromorphology has been cited as an important set of taxonomic characters in gymnosperms, but previous studies have largely been based on small sample sizes. The premise of this study was to understand whether external factors affect cuticular micromorphology of Podocarpaceae. Two example species, Prumnopitys andina and Podocarpus salignus, were studied. Of 21 sampled characters, nine (c.43% of the total) were visually assessed as being moderately reliable or highly reliable for taxonomic discrimination for both species, with an additional six (c.29%) being moderately reliable or highly reliable for only one or other of the example species, and six characters (c.29%) unreliable for both. Seven of the most variable stomatal characters were selected for further analysis to establish whether environmental factors affect them. The relationship between these seven stomatal characters, the environment and climate was analysed using the R ‘vegan’ package and climate data gathered from WorldClim. Our results showed that both species had larger stomata in moist and shady conditions, and a higher density of (smaller) stomata in sunny and drier conditions. An additional novel finding was the presence of stomata on the adaxial leaf surface in 46% of samples of Prumnopitys andina: the first record of adaxial stomata in this species, highlighting the necessity of studying multiple samples of a given species. In conclusion, these results indicate that larger sample sizes than have hitherto been employed in cuticle micromorphological studies are necessary to fully document the amount of phenotypic variation that exists.