Objective: To determine the morphological and molecular characterization of Acanthamoeba isolates from contact lens paraphernalia in Malaysia and to investigate their pathogenic potential based on the physiological tolerance. Methods: One hundred and eighty contact lens wearers donated their contact lens, lens storage cases and lens solutions between 2018 and 2019. The samples were inoculated onto 1.5% non-nutrient agar plates for 14 d. Polymerase chain reaction (PCR) was performed and the amplified PCR products were sequenced and compared with the published sequences in GenBank. The pathogenic potential of positive isolates was further tested using temperature-tolerance and osmo-tolerance assays. Acanthamoeba species were categorized into three distinct morphological groups established by Pussard and Pons. Results: Acanthamoeba was successfully isolated from 14 (7.8%) culture-positive samples in which 11 belong to morphological group II and 3 belong to morphological group III, respectively. The sequencing of 18S ribosomal RNA gene led to the identification of the T4 genotype in all the isolated strains. In vitro assays revealed that 9 (64.3%) Acanthamoeba isolates were able to grow at 42 °C and 1 M mannitol and were thus considered to be highly pathogenic. Conclusions: To the best of our knowledge, this is the first report identifying the Acanthamoeba genotype and their pathogenic potential among contact lens wearers in Malaysia. The potentially pathogenic T4 genotype isolated in this study is the most predominant genotype responsible for human ocular infection worldwide. Hence, increasing attention should be aimed at the prevention of contamination by Acanthamoeba and the disinfection of contact lens paraphernalia.