Books by Neil Broadfoot, Natalie Haynes, Peter May and Nicola White are also up for the Deanston Scottish Crime Book of the Year.
The winner, who will pick up a £1000 prize cheque, will be announced in September as part of the Bloody Scotland Crime Writing Festival, which will be staged in Stirling.
This is the third running of the award: it was won by Malcolm Mackay, with How A Gunman Says Goodbye in 2013, and Charles Cumming in 2012, with A Foreign Country.
Brookmyre's Flesh Wounds, Broadfoot's Falling Fast, The Amber Fury by Haynes, May's Entry Island, A Lovely Way to Burn by Welsh and White's In the Rosary Garden make up the short list.
There are three first novels on the list.
Dom Hastings, manager of the Bloody Scotland festival, said the line up was "strong" and added: "Brookmyre, May and Welsh are well known to both Scottish and international audiences, but it's great to be able to welcome Natalie Haynes, known for her work in television and comedy rather than writing, with her first novel, and brand new writers Neil Broadfoot and Nicola White.
"They've all written fantastic books, which take a variety of approaches to the whodunnit structure, whether they're experimenting with form and darker tones, trying to get inside the mind of a disturbed teenager, creating a dystopian plague-ridden London, examining the murky underworld beneath Edinburgh's political sheen, imagining reincarnation around the Highland Clearances or exploring the restrictions of convent school life.
"The strength and diversity of this year's shortlist proves that Scottish crime writing is still burgeoning and pushing boundaries, whilst enthralling readers."
Brookmyre said: "It is a validation to see Flesh Wounds on this shortlist. I believe it's the most accomplished novel I've written."