Blastocystis sp. is a common enteric parasite of humans and animals associated with inadequate sanitation and poor personal hygiene. Over the years, the Malaysian thriving economy has been facilitated largely by migrant workers from developing countries, and there is concern that diseases endemic to their countries may be imported. Therefore, this study aimed to determine the current status of Blastocystis infection as well as subtypes (STs) from fecal samples among migrant workers in Selangor and Kuala Lumpur, Malaysia. Overall, almost a third of the study cohort (30.9%; n = 68/220) screened were infected with Blastocystis sp. predominantly with ST3 (54.5%; n = 12), followed by ST1 (36.4%; n = 8) and ST2 (9.1%; n = 2). Infection levels was almost similar among the different sectors; manufacturing (32.8%), domestic service (32.3%), and food service (27.3%) with common symptoms for infection included stomach and abdominal pain or discomfort and diarrhea (48.5%; n = 33). None of the socio-demographic risk factors evaluated were significant. Therefore, this study warrants continuous monitoring as well as understanding the impact of transmission among the migrant community with the local population especially those involved in food service sector.