Continuous and simultaneous tracking of change in malaria parasites population structure and change in allele frequencies or point mutation (SNPs) which are associated to antimalarial resistance is very important especially with the increasing use of drugs for malaria elimination at large scale. Malaria Elimination Task Force is implementing P.falciparum elimination operation in 4 townships of Kayin State, Eastern Myanmar. Molecular markers surveillance mechanism has been set up extensively across 1220 malaria posts. Artemisinin resistance mutants, (Kelch 13) and its partner drug resistance mutants (pfdmr1 and plasmepsisn2) mutants proportion is not significantly increased in 4 townships of Eastern Myanmar from 2014-2017, in contrast to Thai-Myanmar border where K13 mutants are outcompeted over the wild type. Falciparum elimination should be accelerated while currently available ACT are effective.