- Y73 sarcoma virus
- Yaba monkey tumor virus
- Yaba-1 virus
- Yaba-7 virus
- Yacaaba virus
- Yam mild mosaic virus
- Yam mosaic virus
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- Yambean mosaic virus
- Yaounde virus
- Yaquina Head virus
- Yatapoxvirus
- Yellow fever virus
- Yellowtail ascites virus
- Yersinia phage L-413C
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- Yogue virus
- Yokapox virus
- Yokase virus
- Yokose virus
- Youcai mosaic virus
- Yponomeuta cognatella NPV
- Yponomeuta evonymella NPV
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- Yponomeuta malinellus NPV
- Yponomeuta padella NPV
- Yucca baciliform virus
- Yug Bogdanovac virus
- Yunnan orbivirus
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