I just had something very similar happen on my Meyer lemon tree. It is strange because from the same branch, it forks into 2 branches. One of these two branches has thorns and no lemons and one of the branches has no thorns and lots of lemons. Throughout the tree there are several branches that are similar. Every branch with thorns has no lemons, but every branch with no thorns has lemons but they emanate from the primary branch.

Is that common for the same branch to have two different kinds of trees mixed up in one. I thought each branch would either be distinctly Meyer lemon or rootstock.

some times a twig will branch off the parent branch that is distinctively different from the parent tree. Cut the undesirable branch off, or top graft it with what you want in place of it. It does not have to be the same as the other branch. what I did 40 years ago as a child I grafted a crab apple twig to my neighbors red delicious apple tree. He was not to observant and I got lots of laughs. The tree succuned to a deisease call chainsawlites and died.

Good luck

Rob,

the tree is not a goner; but if you leave the rootstock to grow, it is much stronger than the scion; so the lemon will not grow.

Toucan,

what you have are most likely what we call watersprouts; usually with larger leaves and big thorns. They are a sign you are probably being too kind to your tree in terms of food. No worries; just prune the watersprout back to the level of the general canopy; and it will revert back to normal growth.