Question: Let's say I play a necromancer and have raised some Skeletons or Zombies using Animate Dead and some Gouls, Ghasts, Wights or Mummies using Create Undead.

When I use a bonus action to command them can I command all the undead I have with single bonus action even though they were created with different spells?

Answer: 
No, you can only command the creatures created by one of the spells when you use your bonus action.
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While both spells state that they require a bonus action, both of them only allow you to command creatures you made with that particular spell.

Here is the relevant rules text for *Animate Dead*:

> 
> On each of your turns, you can use a Bonus Action to mentally Command **any creature you made with this spell** [...]
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As well as the rules text for *Create Undead*:

> 
> As a Bonus Action on each of your turns, you can mentally Command **any creature you animated with this spell** [...]
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No.
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Both spells have this phrasing (emphasis added): 

> 
> On each of your turns, you can use a Bonus Action to mentally Command any creature **you made with this spell** if the creature is within 60 feet of you (if you control multiple creatures, you can Command any or all of them at the same time, issuing the same Command to each one)
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> 
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While the parenthentical clause might make it seem like you can control everything, the first part of the sentence is clear that each use of a bonus action only applies to the creatures from a single spell, and not others. Therefore, if you have undead animated from two separate spells, you will have to control them on different turns, since you only have one bonus action per round.