Currently, the poultry industry is threatened by virulent viruses of endemic disease that can cause major economis losses to this sector. Aim of this research was conducted to epitope prediction from genes encoding F protein of Newcastle Disease Virus (NDV) isolated from waterfowl. Samples of this research collected from cloacal swabs of seventy one waterfowls. Consisting of twenty four domestic swan, thirty three Muscovy ducks, and fourteen domestic ducks form waterfowls in East Java Province,

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... and also positive LaSota Isolates (ATCC). Samples were isolated in embryonated chicken eggs (ECEs) with Specific Pathogen Free (SPF) and identified by HA test and confirmed as NDV by HI test. Positive samples were performed by RT-PCR using forward and reverse primer with target of 699 bp. The sequencing results were analyzed by forward and reverse primer to generate the complete gene. Candidate epitopes were analysed by predictions tools from Immune Epitope Database online program. One epitope was predicted as a peptide vaccine for B cell (HGKILDPGWRPPGARWAPDLLP) from ND/AG3/2018 sample and more likely to be immunogen vaccine candidate based on epitope prediction immunogenic epitope candidates have hisghest log score.