BackgroundSalmonellainfections remain an important public health issue worldwide. Some serovars of non-typhoidalSalmonella(NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulatingS. entericaserovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment.MethodsIn total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data.ResultsForty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified wereS. Cotham (n = 17),S. Give (n = 16),S. Mokola (n = 6),S.Abony (n = 4),S. Typhimurium (n = 4), andS. Senftenberg (n = 1). All 48Salmonellaisolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across severalSalmonellapathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of eachSalmonellaserovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types wereS.Give ST516 andS.Cotham ST617.ConclusionWe found identicalSalmonellasequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one’s health are essential to prevent possible outbreaks.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-023-02901-1.