Species and individuals are different
A species is a biological category containing individual organisms.
A species can become extinct, but it does not experience pain as one conscious being. Individual sentient animals do experience fear, injury and wellbeing.
Why species matter
Species carry unique evolutionary histories and ecological functions.
Extinction is usually irreversible and can alter entire ecosystems.
Why individuals matter
An animal's suffering matters to that animal regardless of whether its species is rare or common.
A common animal does not feel less pain because millions of similar animals exist.
Conflict between levels
Conservation may kill common predators to protect rare prey, remove introduced animals or confine endangered animals for breeding.
Rarity is not moral superiority
Rarity affects conservation priority, but it does not necessarily make each rare animal more capable of suffering than a common one.
Avoid false choices
Habitat protection, prevention, fertility control, barriers and changed human behaviour can sometimes reduce conflict.
When harm may be justified
Some emergencies may involve irreversible harm if no action is taken.
Even then, necessity should be demonstrated and suffering minimised.
Evidence notes
Decisions should assess extinction risk, ecological function, numbers affected, severity and duration of suffering, effectiveness, alternatives and long-term consequences.
Ethical questions
Can many common animals be killed to save a rare species?
Should extinction always outweigh any amount of individual suffering?
Does human responsibility for creating the conflict change what methods are acceptable?
Conclusion
Individual animals are not simply less important than species conservation. They represent a different moral concern.
Species protect evolutionary continuity; individuals possess lives that can go well or badly. Responsible conservation should take both seriously.