There are a whole bunch of manga mystery stories. Here are a very small selection that I think you should check out if you have the chance!
The Kindaichi Case Files by Kanari Yozaburo and Sato Fumiya
This is wildly out of print, but because most of the stories are self contained within each volume, it’s well worth picking up if you find a volume here and there. This is essentially a series featuring the young detective Kindaichi who solves murder mysteries; very much scenarios like you’d find in Agatha Christie novels. Kindaichi is an unassuming youth, but has great powers of perception. The stories are more about the mysteries, than they are about the characters, so if murder mysteries are something you like to read I would definitely recommend checking this one out. Published by Tokyopop.
Utsubora: the Story of a Novelist by Asamiko Nakamura
This is a recently in-print manga, so you should still be able to get your hands on it. This is a beautifully illustrated josei series about a novelist who has some relationship to a young woman who has recently commit suicide by jumping to her death. The mystery is subtly woven in an art house style manga. After you’ve read through it and revealed all of the secrets, you will definitely want to pick it up again. This is one of those mysteries that you get more out of every time you pick it up — which says a lot for a mystery! Definitely would recommend checking this title out. Mature Content. Published by Vertical.
Young Miss Holmes by Kaoru Shintani
This is exactly what it sounds like, a series about a “miss” Holmes. This miss is the niece of the famous detective, who like her famous uncle has a nimble mind and keen observation skills. This is normally a type of series that I don’t like, so I was surprised by how much I enjoyed it. For one, the art in it is beautiful! I would recommend it for that alone. But also, this takes on the concept that miss Holmes is not her uncle’s helper, but her uncle’s competition. She is a tenacious child who wants to best her uncle at solving crimes. They often appear simultaneously at the conclusion, but have come to the correct conclusion in a different way. It’s a delightful read, but recently out of print, so pick it up when you have a chance! Published by Seven Seas.