Despite the economic importance of sorghum in Sudan, its productivity is low. Arbuscular mycorrhizal fungi (AMF) enhance sorghum growth, survival, and nutrient uptake, and their manipulation may have potential in mitigating biotic and abiotic stresses during droughts. However, information on the AMF community in Sudan and the host-AMF specificity at the sorghum genotype level are unknown. We investigated the AMF community structure of 19 sorghum genotypes by next-generation sequencing in a semi-arid region. A total of 102 AMF operational taxonomic units (OTUs) were detected comprising four families: Glomeraceae (85.3%), Claroideoglomeraceae (10.8%), Paraglomeraceae (2.9%), and Diversisporaceae (1%). Among them, appearance ratio of three OTUs (2.9%) belonging to Rhizoglomus was more than 75%, whereas 75 OTUs had lower appearance ratio than 25%, indicating that the AMF community comprised a small number of generalist and a large number of rare OTUs. Non-metric multidimensional scaling and permutational multivariate analysis of variance showed no AMF specificity of the sorghum genotypes. The community assembly was strongly influenced by neutral processes, but 11 OTUs had higher relative frequency than expected by neutral model. The result includes the possibility that adaptability of AMF to soil environment and positive selection by host plant also affect the AMF community assembly. Our work showed that only a few Rhizoglomus species dominated without host plant genotype specificity in a semi-arid Sudanese cropland. Further research on functional analysis of the dominant AMF species may reveal the importance of the dominant AMF species for sorghum cultivation in Sudan.