The American singer was killed in a plane crash in the Bahamas on 25 August, 2001, and to mark the anniversary, Missy has taken to Twitter to share a video of herself writing a handwritten note to Aaliyah.
It reads: ''Aaliyah, we miss you so much. But your legacy will live on forever and ever!''
The heartfelt tribute was captioned: ''Aaliyah (Babygirl) I can only imagine how great you would be today winning oscars [winking emoji] & creating sick music & still setting fashion trends! Your mom & brother @RAD_6 & your fans been holding it down 4 u [love heart emoji] you will always be A One in A Million sleep peacefully angel Babygirl [praying emoji] (sic)''
Missy, 47, previously revealed that as well as being a hugely talented singer and actress, Aaliyah was also incredibly funny.
She shared: ''Aaliyah, she was like a comedian. She always wanted to laugh.''
The duo first worked together during the mid-1990s and Missy was initially fearful that the singer - who passed away at the age of 22 - would be a diva.
However, they immediately struck up a friendship and Missy loved spending time with the '4 Page Letter' hitmaker in the recording studio.
Recalling their first meeting, Missy - who first worked with Aaliyah on her 1996 album 'One in a Million' - said: ''We were nervous when we first worked with her because nobody knew who we was.
''She came in and was so warming; she made us immediately feel like family.''
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