Pulicaria crispa, a xerophytic species of the family Asteraceae, demonstrates significant ecological adaptability across arid regions of Saudi Arabia. This study aimed to investigate the genetic and palynological diversity among four geographically distinct populations of P. crispa using a combined approach of morphological, palynological and molecular analyses. Pollen grains were extracted from mature anthers, acetalized and examined under light and scanning electron microscopes to measure key characteristics such as polar and equatorial diameter, aperture type and exine ornamentation. Additionally, genomic DNA was isolated from fresh leaf tissues and amplified using ISSR and ISJ molecular markers to assess genetic variation. A total of 134 ISSR bands and 112 ISJ bands were generated, with ISSR markers showing higher polymorphism (79.4 %) than ISJ (62.5 %). Morphological and palynological features displayed significant inter-population variability. Mantel tests revealed a moderate correlation (r = 0.52, p < 0.05) between molecular and morphological distances, indicating potential adaptive divergence. The King Abdulaziz Royal Reserve population exhibited the highest genetic and palynological diversity. These findings underscore the value of using integrated molecular and palynological tools to assess biodiversity in desert-adapted plant species, highlighting the evolutionary significance of environmental pressures shaping P. crispa populations. This work contributes to the ecological and conservation understanding of xerophytic flora in the Arabian Peninsula.