The whitefly vector remains a key factor in the continued prevalence of Cassava Mosaic Disease (CMD) and the threat of Cassava Brown Streak Disease (CBSD) to unaffected regions in Central and West Africa. Cross-border surveillance is critical because borders serve as the first entry point for pests and pathogens. This study identified the whitefly genotype groups prevalent in cassava-producing locations along the Nigeria–Cameroon border, and their associated Cassava mosaic begomovirus (CMB) strains. Mitochondrial cytochrome oxidase I (mtCOI) gene sequencing (97 sequences), sequence alignment, and phylogenetic analysis revealed several Bemisia tabaci (Gennadius) genotypes alongside Bemisia afer (Priesner & Hosny). B. tabaci sub-Saharan Africa 1-subgroup 1 (SSA1-SG1), SSA2, SSA3, and Mediterranean (MED) genotypes were recorded in Nigeria and Cameroon. MED and SSA3 genotypes were predominant in the North–East and South–South regions of Nigeria, respectively, while SSA2 and SSA3 were the predominant genotypes on the corresponding side of the Cameroon border. CMB-specific PCR amplification revealed the presence of African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) in several B. tabaci genotypes and in B. afer. These findings demonstrate a distinct vector distribution pattern across the Nigeria–Cameroon border and emphasize the need for continued cross-border cassava virus surveillance.