Seems that Marisa is now a Witch/Youkai so she outlived Reimu and the child is her daughter/descendant. I'd imagine the later since the child doesn't recognize Marisa which I'd find weird if it was her daughter.
Well it doesn't show how many years have passed, she may be the 10th Hakurei successor since Reimu, so she may only know Marisa as the witch youkai who squats the temple once every year
Plus, the little shrine maiden said that Marisa was "a 100-something grand youkai", which makes the second-half of this doujin takes place more than a century after present time (first-half).