Global efforts to control and eliminate malaria are threatened by the emergence and spread of antimalarial drug resistance. The World Health Organization recommends surveillance of molecular markers of resistance as a complementary approach to therapeutic efficacy studies. Here, we report the first regional analysis of malaria drug resistance markers from genomic surveillance across six southern African countries spanning diverse transmission intensities and geographies. Dried blood spots, collected from rapid diagnostic test-positive individuals in Angola, Eswatini, Namibia, and Zambia in 2023, Mozambique in 2022, and South Africa between 2022 and 2024 using a standardized collection method, were analyzed using a Plasmodium falciparum targeted amplicon sequencing protocol. The distribution of resistance markers was spatially heterogeneous. Markers of artemisinin partial resistance (ART-R) were rare, never detected in >1.3% of samples from any country. However, over 30% of samples from eastern Namibia and Zambia's Western and Central Provinces carried the candidate kelch13 P441L ART-R marker. Other ART-R markers (kelch13 R515K, P553L, P574L, A675V) were detected at low frequencies in all countries except Mozambique. The wild type mdr1 N86 allele, potentially associated with reduced lumefantrine susceptibility, was near fixation across all countries. The sulfadoxine-pyrimethamine (SP) resistance dhps-dhfr quintuple mutation was approaching fixation in most districts, except northern Angola, where dhps K540E prevalence was lower and the crt K76T chloroquine resistance marker more frequently detected. This pronounced spatial heterogeneity underscores the need for timely high-resolution local resistance data generation and sharing to safeguard antimalarial drug efficacy and guide malaria control and elimination strategies across the region.