There is a significant gap in our knowledge of the intraspecific morphological variability in freshwater fish, although such data are crucial for understanding species diversity. Here we use the killifish Aphaniops stoliczkanus (Day, 1872; Aphaniidae: Cyprinodontiformes), which is a widespread but poorly known freshwater species in the Middle East, to investigate variability in morphologi cal traits within and between its populations. As otolith morphology is known to evolve on ecological timescales and can signal the presence of cryptic line ages, a special focus lies on otolith variability. Based on samples from six popula tions in northern Oman, we found that variation in pigmentation, disparities in body shape and otolith variability can be associated with distinctive environmen tal conditions. The unique otolith shape of A. stoliczkanus from a hot sulphuric spring (Nakhal) suggests that a cryptic lineage may have emerged there. Our new data can serve as a benchmark for future studies on the diversity of Aphaniops and other Aphaniidae and help to clarify whether cryptic diversity is present in some lineages. Moreover, our data can serve as an actualistic model for studies on fossil fishes, in which morphological characters provide the only accessible data source for taxonomic and phylogenetic interpretations.