Background: Imported malaria represents a major threat to the prospect of elimination and eradications in areas where transmission has been interrupted. In the past two decades many countries in the Arabian Peninsula have successfully interrupted local transmission. However, this success is jeopardized by the massive influx of migrant workers from endemic areas. The present study examined the source of imported Plasmodium falciparum into Qatar and assessed its genetic diversity and ability to transmit if vector control relaxes. Methods: P. falciparum isolates were collected from 94 imported cases reported to Hamad Medical Corporation, Qatar. Parasite density was estimated using qPCR of 18S rRNA. Early and late gametocyte stages were detected and quantified using qRT-PCR. Ten microsatellites representing seven chromosomes of P. falciparum were genotyped using PCR and fragment analysis. The genetic data was analyzed to assess genetic diversity and genetic relatedness of imported parasites in few foci, where transmission occurs, in the region. Results: Ninety-Four P. falciparum isolates reported by migrants from Africa (n = 77), the Indian Subcontinent (n = 13) and unidentified origin (n = 4) were examined. The median parasitaemia among imported cases from the Indian Subcontinent (99571.8 parasites per ml blood) was 1.13 folds higher than that from Africa (88503.9 parasites /ml of blood). A large proportion of imported cases (50%, 27/54) carried mature gametocytes, indicative by presence of Pfs 25 transcripts and many (13%, 7/54) carried early gametocytes, indicative by presence of Pfpeg4 transcripts. However, many isolates (37%, 20/54) carried a mixture of early and late gametocytes transcripts (Pfpeg4) and (Pfs25). A high degree of allelic diversity (expected heterozygosity) was observed among parasites from both continents. However, the number of effective alleles was higher among isolates originating from Africa compared to the Indian Subcontinent. A high multiplicity of infection and mild, but statistically significant linkage disequilibrium, was seen among P. falciparum populations from both regions. Low Fst estimate was seen between parasites in both sites and with Saudi Arabia and Yemen were local parasite transmission occur suggesting lack of geographical differentiation. Conclusion: Imported P. falciparum into Qatar is genetically diverse, with no evidence of genetic isolation. The presence of transcripts of early and late gametocyte specific genes, signifies the ability of imported malaria parasites to transmit, when vector control measures relaxes in receptive areas. There is necessity to implement molecular surveillance to ensure higher efficiency measures to prevent reintroduction of malaria.