This article studies the morphological parameters of vegetative and generative organs of different age groups of Crataegus ambigua from four populations in Western Karatau (Mangistau region, Kazakhstan). In this study, we examined four populations: Sultan Epe, Karakozaiym, Emdikorgan, and Samal, all located in various gorges of Western Karatau. Several phylogenetic inference methods were applied, using six genetic markers to reconstruct the evolutionary relationships between these populations: atpF-atpH, internal transcribed spacer (ITS), matK, psbK-psbI, rbcL, and trnH-psbA. We also used a statistical analysis of plants' vegetative and generative organs for three age groups (virgin, young, and adult generative). According to the age structure, Samal has a high concentration of young generative plants (42.3%) and adult generative plants (30.9%). Morphological analysis showed the significance of the parameters of the generative organs and separated the Samal population into a separate group according to the primary principal component analysis (PCoA) coordinates. The results of the floristic analysis showed that the Samal populations have a high concentration of species diversity. Comparative dendrograms using UPGMA (unweighted pair group method with arithmetic mean) showed that information gleaned from genetic markers and the psbK-psbI region can be used to determine the difference between the fourth Samal population and the other three.