Aedes albopictus (Skuse) is an important vector of chikungunya, dengue, yellow fever and Zika viruses. In the absence of anti-viral medication and with limited availability of a commercial vaccine for public health use, vector control remains an effective means for reducing Aedes-borne disease morbidity. Knowledge about genetic mutations associated with insecticide resistance (IR) is a prerequisite for developing rapid resistance diagnosis, and the distribution and frequency of IR conferring mutations is important information for making smart vector control decisions. Partial DNA sequences of domain II and domain III of Ae. albopictus voltage gated sodium channel (VGSC) gene were amplified from a total of 426 individuals, collected from 17 sites in the Beijing municipality. These DNA fragments were sequenced to discover the possible genetic mutations mediating knockdown resistance (kdr) to pyrethroids. The frequency and distribution of kdr mutations were assessed in the 17 Ae. albopictus populations. The origin of kdr mutations was investigated by haplotype clarification and phylogenetic analysis. Sequence alignments revealed the existence of multiple mutations (V1016G, I1532T, F1534S and F1534L) in VGSC. The highest frequency of the mutant 1016G allele (0.647) was found in Haidian, while 1016G was not detected in Huai Rou, Yan Qing, Ping Gu and Shun Yi. The frequency of 1532T was highest (0.537) in the population from the Olympic Forest Park (OFP, Chao Yang District), but not detectable in Huai Rou and Mi Yun. Two mutations were observed at codon 1534 with different distribution patterns: 1534L was only found in Tong Zhou (TZ) with a frequency of 0.017, while 1534S was distributed in TZ, OFP, Fang Shan, Da Xing and Shi Jing Shan with frequencies ranging from 0.019 (OFP) to 0.276 (TZ). One 1016G, one 1532T, one 1534L and two 1534S haplotypes were identified. Multiple mutations (V1016G, I1532T, F1534L/S) in VGSC were found in Ae. albopictus in Beijing. This represents the first report of V1016G in Ae. albopictus. Sequence alignment and phylogenetic analysis revealed multiple origins of 1534S. The spatial heterogeneity in distribution and frequency of kdr mutations calls for a site-specific strategy for the monitoring of insecticide resistance. The relatively high frequencies of V1016G warn of a risk of pyrethroid resistance in mosquitoes in the urban zones.