Apis cerana is widely adapted to vast areas that stretch from Russia to Sundaland (Indonesia) through Palawan in the Philippines. By using mitochondrial DNA of the cytochrome oxidase subunit 1 (COX1) gene, the cytochrome oxidase subunit 2 (COX2) gene, and the COX1-COX2 intergenic regions (IGS), as well as the nuclear major royal jelly protein 2 (mrjp2) gene, we aimed to explore the number of new haplotypes of A. cerana in Indonesia and the genetic variations of A. cerana in Indonesia, particularly between Sundaland A. cerana with the Moluccas and West Papua. These studies found three main findings; the first is the 11 A. cerana new haplotypes in total for the COX1, COX2, IGS, and mrjp2 gene sequences. The maximum likelihood phylogenetic tree agreed with the haplotype cluster. Apis cerana in West Papua and the Moluccas clustered in the same clade with the Sundaland A. cerana from Java, Banten, and Belitung, that suggests common origin of these bees. The third finding is genetic distances of COX1 gene between A. cerana in Java and those from West, East, South Kalimantan, Sabah, and Sarawak were approximately 4% which is similar to genetic distance between Indonesian A. cerana (A. cerana javana) and East Asia (A. cerana cerana and A. cerana japonica). The genetic distance also proved the separation of the Indonesian A. cerana lineage with the Indo-Malayan lineage (Sabah, Sarawak, and Kalimantan) from previous studies. This result gives rise to the possibility of the emerging new subspecies of A. cerana in Kalimantan.

蜜蜂广泛适应从俄罗斯到巽他兰（印度尼西亚）到菲律宾巴拉望的广大地区。通过使用细胞色素氧化酶亚基 1 (COX 1 )基因、细胞色素氧化酶亚基2 (COX 2 )基因和COX1 - COX2基因间区域 (IGS) 以及核主要蜂王浆蛋白 2 ( mrjp2）的基因，我们的目的是探索新的单倍型数A.蜜蜂在印尼的遗传变异东方蜜蜂在印尼，尤其之间巽他大陆东方蜜蜂与摩鹿加群岛和西巴布亚。这些研究发现了三个主要发现；第一个是COX1、COX2、IGS和mrjp2基因序列的总共11个A.cerana新单倍型。最大似然系统发育树与单倍型簇一致。西巴布亚和摩鹿加群岛的蜜蜂与来自爪哇、万丹和勿里洞的 Sundaland A. cerana聚集在同一分支中，这表明这些蜜蜂的共同起源。第三个发现是A. cerana之间COX1基因的遗传距离在Java和那些来自西，东，南加里曼丹，沙巴，沙捞越和约为4％，这是类似于印尼之间的遗传距离东方蜜蜂（A.蜜蜂javana）和东亚（A.中华蜜蜂和东方蜜蜂粳稻）。遗传距离也证明了印度尼西亚A. cerana谱系与印度-马来亚谱系（沙巴、砂拉越和加里曼丹）与先前研究的分离。这一结果增加了在加里曼丹出现A. cerana新亚种的可能性。