Maize is the most important source of energy in Zambia and it is the most commonly grown crop. Over the years, the Zambian public maize breeding programme has a collection of about 800 maize inbred lines for hybrid breeding. However, these inbred lines have not been characterised. Therefore, a study was conducted on a sample of 153 inbred lines with the objective of assessing the genetic diversity and determining the population structure. The genetic distances of 153 inbreds ranged from 0.00 to 0.64, while gene diversity ranged from 0.10 to 0.37. All SNPs used had good differentiating power, with minor allele frequency (MAF)>0.2. The 153 inbred lines were divided into nine populations as inferred by STRUCTURE analysis, with 59% of variation among inbreds within a population being retained with between population variation explaining 26%. The populations were highly significantly differentiated, thereby indicating the existence of genetic structure for the southern African maize inbred lines. Inbred lines that might result in heterotic response were identified, while very close inbreds with similar pedigree can be used for the development of modified single crosses. The development of a corset from the collections is proposed as this will form a basis for the formation of divergent populations for hybrid breeding.