Usually we use
In the morning
Both of them represent time but why do we use different prepositions?
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A general rule, is that words that are used with the preposition "the", use "in the", wheras if "the" is not needed, then use "at". Night is the main exception to this rule:
"In the night"
Both make sense.
I don't know the origins or reasons for this, but it probably just developed over time like many language features.