The black-backed jackal has proven difficult to study in the wild due to its elusive behaviour. As a rabies vector and predator of livestock, understanding dispersal patterns and population structure is of importance when considering the management of this species in South Africa’s rural areas. We have characterised a suite of six cross-species microsatellite markers suitable for this purpose and present a method to isolate suitable quantities of host DNA from faeces in order to undertake endpoint PCR. Allelic dropout and null allele frequencies were shown to be negligible for all loci. No evidence of selection could be detected at any of the loci examined. The genotype frequencies of the total sampled population were tested for concordance with Hardy–Weinberg equilibrium. No significant deficit of heterozygote individuals was detected globally when tested by locus and marker set. An excess of heterozygosity was recorded at three loci within a single study site. The total inbreeding coefficient F_ST was calculated at 3% across the sampled population. The average DNA copy number recovered from faecal deposits was quantified using a qPCR-TacMan reporter probe method. The results of this study indicate that the quantity of DNA recovered from faeces was sufficient to undertake endpoint PCR.