AbstractEven though pollen and seed dispersals are some of the important factors that determine tree species survival across landscapes, gene dispersal data of important tropical dryland tree species such asAcacia senegalthat are undergoing various population disturbances remain scarce. Understanding patterns of gene dispersal in these ecosystems is important for conservation, landscape restoration and tree improvement. We investigated pollen and seed mediated gene flow in twoA. senegalpopulations of contrasting state (less disturbed and heavily undisturbed) using nine microsatellites and 128 genotyping‐by‐sequencing single nucleotide polymorphism (SNPs) multilocus genotypes of two growth stages (juvenile and adult trees) and their spatial locations. We performed parentage assignments using likelihood approach and undertook spatial genetic structure (SGS) analyses for the two growth stages through correlation among kinship coefficients and geographical distances between pair of individuals. The SNPs showed higher resolving power and assignment rates than microsatellites; however, a combination of the two marker‐types improved the assignment rate and provided robust parentage assessments. We found evidence of long‐distance (up to 210 m) pollination events for both populations; however, the majority of seed dispersal was found closer to the putative maternal parent. On average, parentage analysis showed high amounts of pollen (40%) and seed (20%) immigration in both populations. Significant positive SGS was found only for the adult cohorts in the less disturbed population for distance classes 20 and 40 m, indicating historical short‐distance seed dispersals. Our results suggest long‐distance gene flow within the species and we recommend conservation of remnant and isolated populations or individual trees to promote genetic connectivity.