Save one Species

I suppose the question implies that you can save one species, but the remaining ones doesn't change their status. Hence, common non-threatened, even invasive plague species like honeybees and humans would be out of the contest.

I would choose then the species of megafauna that is in the most inmediate brink of inminent and unavoidable extinction: the vaquita (Phocoena sinus).
 
Mine would be, obviously, the Philippine eagle.

Reason: it's critically endangered, it's the largest of all powerful eagles, the most colorful, a breeding program already exist, and protecting the eagle is protecting the habitat.

By saving this apex predator hundreds of other species will be protected too. So in the case one can only pick up one species, pick up the right one (the one who needs large habitat requirements with lots of other smaller species).
 
Like Neil chace said, I would also choose to save the honey bee, more specifically, the Western Honey Bee. If it was just humans and bees on Earth, we could still probably survive by eating the plants that the bees pollinate and eat the honey they produce. Choose almost any other species, and the planet will fall apart, by wiping out the plant life, and most likely causing the extinction of both humanity, and the species we chose to survive.

I would have to disagree. Apis mellifera is native to the Palearctic Realm only. It may be true that humans depend on this particular species of bee to pollinate our main food crops, but this is because many of them also come from Europe or the Middle East.
Think about it. The flora and fauna of the rest of the world has existed just fine without the Western Honey Bee (and often better than with it once it were introduced for agricultural purposes). These places have had their own native insect pollinators (which are, unfortunately, often overshadowed by honey bees in conservation discourse). For example, studies show that while Western Honey Bees do no good to North American ecosystems, they can potentially harm some wild bees and native plants. Additionally, despite Colony Collapse Disorder affecting lots of, (free-roaming, I must emphasize) Western Honey Bees are abundant enough in both their native and non-native ranges that they are considered Least Concern and therefore do not need saving as much as is often said. The extinction of the Western Honey Bee would harm some Eurasian ecosystems, worrying this much about a Least Concern and possibly invasive agricultural species seems rather anthropocentric to me. While bees in general are extremely important, the main concern with the Western Honey Bee in particular is, from a worldwide perspective, more agricultural than it is ecological.
 
Mine would be, obviously, the Philippine eagle.

Reason: it's critically endangered, it's the largest of all powerful eagles, the most colorful, a breeding program already exist, and protecting the eagle is protecting the habitat.

By saving this apex predator hundreds of other species will be protected too. So in the case one can only pick up one species, pick up the right one (the one who needs large habitat requirements with lots of other smaller species).
this would be my answer too
 
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