A total of 220 chickens were collected from different commercial broiler farms (1- 30 days old chicks) at Dakhlia Governorate and inspected for mycotic infection. Organ samples were taken from 100 diseased chicken and 120 freshly dead ones (lung, air sac, crop, liver and brain from each chicken) after clinical and postmortem examination. All samples were
cultured on specific media for fungi and examined macroscopically and microscopically together with the biochemical tests for identification of the fungi. The genotypic characters of fungi were done by using PCR. The results of fungi isolation revealed that 190 isolates (35.85%) out of 530 samples were positive for fungi; represented as 122 positive samples
(36.97%) from diseased chickens and 68 positive samples (34 %) from freshly dead ones. Positive lung samples were 56 (29.47%) followed by 47 (24.74%) from liver and air sac samples while, 40 (34.78%) were from crop samples. Meanwhile isolates of Aspergillus (A.) spp. were higher than those of Candida albicans (C. albicans); A. fumigates was the frequently isolated spp. 87 (45.79%) followed by A. flavus 47 (24.74%); A. niger 38 (20%) and C. albicans 18 (9.47%), respectively. The molecular characterization of Aspergillus (A.) spp. and C. albicans was carried out by using PCR followed by sequencing of the PCR products. The identification of Aspergillus spp. and C. albicans by PCR was based on using 18S and 28S rDNA as target DNA. The sequences obtained for A. flavus isolate SR6 internal transcribed spacer 1, partial sequence of 28S ribosomal RNA gene obtained were more than 97% identical to the corresponding Gen Bank sequences. Finally, we concluded that Aspergillus spp. and C. albicans were the most isolated fungi and they were the most important causes of mould infection and candidiasis in broiler chicken farms.The characterization of DNA sequences was used as a diagnostic method to distinguish between different Aspergillus and different yeast.