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So, I was just reading through the rules, and couldn't find this in the transport rules(I might have over looked it) but can I put two, 5 man squads in a transport that has a capability of 10?

No

the rules state that A unit may embark... it never states that 2 or units may do so

Exceptoin is Space Marines and Combat Squads for, I beileve, Dedicated Transports.

 HCMistborn wrote:
So, I was just reading through the rules, and couldn't find this in the transport rules(I might have over looked it) but can I put two, 5 man squads in a transport that has a capability of 10?

Short answer: no.
Long answer: sometimes.

A squad of marines that is combat squadding can start both halves in their transport. But once they get out, only one can get back in at a time.

Super heavy transports can embark multiple units.

Thank you, that answers my question. I must've over looked that somehow.

Clearly answered under 'Transport Capacity' (pg. 80, main rulebook) in bold print:

A Transport can carry a single Infantry unit and/or any number of Independent Characters (as long as they are also Infantry), up to a total number of models equal to the vehicle's Transport Capacity

Any exceptions will be found in either the vehicle's rules (Stormraven) or the army's special rules (Combat Squads).

Rulebook, pg.80, second sentence under “Transport Capacity” specifies a single unit.

Combat squad rules are in the SM codex, pg. 188. Re-reading them, it looks like you might be able to re-embark into a transport together. Huh, I thought once you got out, you were done sharing.

...And ninja’d on the rules cite.

 Nevelon wrote:
Rulebook, pg.80, second sentence under “Transport Capacity” specifies a single unit.

Combat squad rules are in the SM codex, pg. 188. Re-reading them, it looks like you might be able to re-embark into a transport together. Huh, I thought once you got out, you were done sharing.

...And ninja’d on the rules cite.

It used to be that it was only during deployment that both could be in the Transport. The current codex changed it.