Analysis of mitochondrial DNA (mtDNA) was carried out using 38 Kalahari Red (KR) goats randomly sampled from a flock imported into Nigeria in 2011 by the Federal University of Agriculture, Abeokuta, as an initial step to investigate the genetic structure of the breed, due to limited information on the breed. Apart from estimating genetic diversities, phylogenetic analysis to elucidate maternal lineages, relationship with wild goats as well as Tajima's D and Fu's Fs statistics were computed to test the departure from constant population size under the neutral model. The first hypervariable (HV1) region of mtDNA (481 bp) sequenced from 38 goats represented 11 haplotypes. Polymorphism of HV1 fragment was high, haplotype and nucleotide diversities were 0.869 ± 0.030 and 0.0299 ± 0.0067, respectively. Maximum-likelihood tree constructed with 11 haplotypes and 22 reference haplotypes representing six haplogroups worldwide revealed that five out of 11 haplotypes belong to haplogroup A, whereas six haplotypes belong to B. KR population clustered with Capra aegagrus as its wild ancestor. There was evidence of mitochondrial footprint that reflected past population decline based on positive and significant Fu's Fs estimate (6.283; P < 0.01). The mtDNA data did not however show that genetic variability of the breed has drastically reduced on account of population reduction. The information obtained is strategic to utilization and conservation of the population.