Background Successful malaria control programs have interrupted local malaria transmission in almost all the Gulf Cooperation Council (GCC) countries. However, a massive influx of imported malaria via migrant workers from endemic areas sustains a threat for the re-introduction of local transmission. Here we examined the origin of imported malaria into one of the GCC countries (Qatar) and assessed the extent of genetic diversity, and carriage of drug resistance genes of imported Plasmodium falciparum and it’s potential to re-introduce the disease. Methods We examined imported malaria reported in Qatar, between 2013 and 2016. We focused on P. falciparum infections and estimated total parasite and gametocyte density using qPCR and qRT-PCR, respectively. In addition, we examined ten neutral microsatellites and four drug resistance genes, Pfmrp1, Pfcrt, Pfmdr1 and Pfkelch13 , to assess the extent of diversity of imported P. falciparum and its potential carriage of drug resistance genotypes respectively. Results The majority of imported malaria comprised P. vivax , while P. falciparum and mixed species infections ( P. falciparum /P. vivax ) were less frequent. The main origin of P. vivax was the Indian subcontinent, while P. falciparum was most apparent among expatriates from Africa. Imported P. falciparum was highly diverse carrying multiple genotypes as well as early and late gametocytes. We observed a high prevalence of SNPs implicated in drug resistance among imported P. falciparum , with some novel SNPs in Pfkelch13 . Conclusions The high influx of genetically diverse P. falciparum, with multiple drug resistance marker gene mutations and high capacity of producing gametocytes, sustains threat for re-introduction of drug resistant malaria into GCC countries. This scenario highlights the impact of current globalisation of movement of humans in reintroducing malaria infections to areas targeted for elimination.