The Allium subgenus Amerallium Traub encompasses a diverse and ancient lineage of approximately 140 species distributed disjunctly across the Mediterranean Basin, North America, and Western Asia. Phylogenetic and cytogenetic evidence supports its origin in the Old World, with North American taxa sharing a conserved base chromosome number (x = 7), unlike the broader variation observed in Old World taxa (x = 7–11). Despite its evolutionary significance, the North African representatives of this subgenus remain insufficiently studied, and their taxonomic boundaries are often unclear. This study focuses on elucidating the chromosomal diversity and phylogenetic structure of Amerallium species in Algeria, with the aim of clarifying species delimitations and identifying key evolutionary processes. A total of 80 wild populations belonging to six taxa (A. subhirsutum, A. subvillosum, A. roseum, A. odoratissimum, A. triquetrum, and A. chamaemoly) were sampled along an environmental gradient from coastal to arid regions in northern Algeria. Karyotype analyses uncovered a high degree of variation, with six distinct cytotypes (2n = 14, 16, 18, 22, 28, 32) corresponding to four basic chromosome numbers (x = 7, 8, 9, 11). Polyploid forms were limited to x = 7 and x = 8. Significant disparities in karyotype asymmetry indices were detected, particularly among polyploids. Molecular phylogenies based on ITS rDNA and chloroplast sequences (trnL–trnF, trnD–trnT) resolved a distinct North African clade, clearly separated from other Old and New World lineages. These findings emphasize the unique evolutionary trajectory of North African Allium species and underscore the role of chromosomal dynamics, particularly polyploidy and dysploidy, in their diversification. Further genomic investigations are needed to fully understand the origins and complexity of this lineage.