Improved cultivars are developed by the breeders due to the variability in characters and availability of redundant diverse genotypes. Many pepper varieties exist in the cultivated land and waste sites in southwest Nigeria but very few had been recommended for breeding and crop improvement. This study was aimed to characterize accessions of pepper varieties from southwest Nigeria using morphological characters with a view to select genotypes with desirable morphological traits for breeding, crop improvement and hybridization. Thirty accessions were characterized using 45 morphological (27 qualitative and 18 quantitative) characters. Qualitative characters were recorded while quantitative characters were measured. Descriptive statistics, Principal component analysis (PCA), correlation coefficients and Principal coordinate analysis (PCoA) were carried out using IBM SPSS software package 20.0 version. A wide diversity was observed and measured among pepper varieties on vegetative and reproductive morphological characters. Hence the following genotypes C. frutescens var. maxima (AOS009, AOS023, AOS033), C. annuum var. glabrisculum (AOS010, AOS036), C. frutescens var. baccatum (AOS038), C. frutescens var. chacoense (AOS028), C. frutescens var. minima (AOS040) and unknown variety (AOS019) were identified and are hereby suggested for hybridization and recommended to breeders for crop improvement.