Aflatoxins are secondary toxic metabolites produced by aspergilli. Aspergillus flavus is one of the major aflatoxins producing specie. Present study was conducted to enumerate mycoflora of poultry feed and aflatoxin production potential of A. flavus. Home mixed and commercial poultry feed (n=20, each) were processed for determination of fungal load and isolation of mycoflora. Isolates were identified by culture and microscopic characters. Thin layer (TL) and high-performance liquid chromatography (HPLC) were used for screening, identification and quantification of aflatoxins produced by A. flavus respectively. A. flavus were confirmed by specie specific polymerase chain reaction (PCR). Isolation frequency of different genera, Aspergillus species and toxigenic A. flavus was calculated. The fungal count in home mixed feed was 2x10 2 to 1.6x10 4 CFU/g whereas, in commercial poultry feed from 2x10 1 to 6x10 3 CFU/g. Aspergillus was the most prevalent genus in home mixed and commercial feed followed by Mucor. Among aspergilli, the highest percentage was of flavus (95%) followed by A. niger (75%), A. fumigatus (15%) and A. terreus (5%). A total of 32.61 percent (223/685) aflatoxin producing A. flavus from commercial and 16.67 percent (23/140) from home mixed feed were detected by TLC. These aflatoxins (AFs) were identified as AFB1 and AFB2 and AFG1 by HPLC. Amplicon (500 bps) of A. flavus was observed on 2 percent agarose gel. It was concluded that poultry feed may be a source of transmission of disease producing fungi and aflatoxins to poultry birds and human beings. ©2019 PVJ. All rights reserved Key words: Aflatoxin Aspergillus flavus commercial poultry feed High performance liquid chromatography Home mixed poultry feed Polymerase chain reaction To Cite This Article: Sana S, Anjum AA, Yaqub T, Nasir M, Ali MA and Abbas M, 2019. Molecular approaches for characterization of aflatoxin producing Aspergillus flavus isolates from poultry feed. Pak Vet J, 39(2): 169-174. http://dx.