The apple are 【on】the tree.
on the tree和on the tree译成汉语都是“在树上”之意,但所表示的含义是不一样的.in the tree多指外界的事物或人在树上,而非树木自身所长；而on the tree则多指树自身所有,长在树上的东西.请辨明：
树上有一些鸟.
There are some birds in the tree.
树上（长）有许多又大、又红的苹果.
There are many big,red apples on the tree.
此外想提一句,你提供的句子有问题,应该是：
The apples are 【on】the tree.
The apple is 【on】the tree.