The free living amoebae cause various infections such as Acanthamoeba keratitis, granulomatous amoebic encephalitis, primer amoebic meningoencephalitis in humans and animals. The free living amoebae Acanthamoeba, Balamuthia mandriallis, Naegleria fowleria and Sappinia species that cause disease in humans have been isolated from many environmental materials until today. However, no isolation has been reported from the filters of the air conditions from the houses used for ventilation. The aim of this study was toinvestigate the existence of free living amoebae using molecular methods in the filters of air-conditions used in the study living area of the people. A total of 30 dust samples were taken from the filtersof air-conditions in Adana and Gaziantep province of Turkey. DNA isolation of the dust samples was performed using the DNeasy PowerSoil kit (Qiagen, Germany) and polymerase chain reaction was done with specific primers of Acanthamoeba spp., B.mandriallis, N.fowleria and Sappinia species. As a result of this study, Acanthamoeba spp. was determined as 33.3% (5/15) and B.mandriallis was determined as6.6% (1/15) in Adana province. On the other hand, Acanthamoeba species was determined as 26.6% (4/15) and B.mandriallis was determined as 13.3% (2/15) in Gaziantep province. N.fowleria and Sappina species were not detectedin both of the cities. DNA sequence analysis was performed for the confirmation of the species and 99% of the results were similar to the other species in GenBank. The rates of Acanthamoeba castellanii and Acanthamoeba griffinii (T3) were determined as %66.6 (6/9) and 33.3% (3/9), respectively by DNA sequencing. Distribution of Acanthamoeba species according to the cities were 33.3% (3/9) for A.castellanii and 22.2% (2/9) for A.griffini in Adana. It was 33.3% (3/9) for A.castellanii and 11.1% (1/9) for A.griffini in Gaziantep. There was no significant difference in the distribution of the parasite species among cities (p > 0.1). It is important to raise awareness of the diseases caused by free living amoebae among people. Acanthamoeba species have been reported frequently from environmental materials in Turkey, but B.mandriallis has not been reported from any environmental sample since this study. The presence of B.mandriallis has been reported in the air-conditions of houses in this study. This result shows that people have risk in terms of illness of free living amoebae in living areas. Our study emphasized that firstly the health personnel and then the people should be informed about the deadly parasites and the cleaning of the air conditions should be done in certain periods.