Rust mites: A ubiquitous pest, present on many a ship, they get their nutrients by eating the plentiful oxidized metal aboard airships and scrap. Scourge of the engineer, as their excretement speeds up the rusting of a component. Hard to spot, harder to kill, the best defense is preventative maintenence and taking care of your ship.
Hydrogen flies: Often present in balloons, these flies rise to great heights throgh the use of hydrogen sacks on their backs, almost like miniature airships. Once they reach a sufficient height, they tuck in, and let the wind carry them to new airspace. Once in flight, the fly gives birth, laying many eggs filed with lifting gas, sacrificing its own lift in the process.
Engine spiders: Spiders adapted to spinning webs in complicated gear work. Extremely strong thread. Once again, the Engineer's bane, as clearing them out can take some time, and they like to bite.
Air barnacles: Exactly what it says on the tin. They like the bottom of Airships, and spread through airborne 'spores'.
Sniffer animals: Any animal with a keen sense of smell that has been trained to recognize leaking Hydrogen. Also helps repel boarding actions.
Desert goats: After the mountains that were once desert disappeared, many animals were trapped in their new, harsh environment. Mountain goats were ne of them. As is well known, goats will eat practically any thing. Desert goats can and will eat practically anything. Thus includes other animals, and you. Be very scared.
Blue Duck: A duck species that quacks nigh constantly, and have been spotted in large swathes of open sky. Still amphibious, but better adapted for great heights than your average duck. Suspected to prey on unsuspecting crews.
Sky Kraken: Even more mysterious than Sky whales, the Sky Kraken is only ever spoken of in hushed tones. Scarcely believed, as the Sky sailors who have survived encounters are usually a little loopy afterwards. Their tall tale doesn't help much, either.
Sky sharks: basically sharks, but airborne through the use of hydrogen bladders. I figured we needed some kind of Sky predator, so why not.