With the history, infrastructure and necessary work ethic to make things happen, Glasgow is globally renowned as an epicentre of independent, cutting-edge music.

Edinburgh, on the other hand, has always played second fiddle to its west-coast cousin. Wealthier and more middle-class, it's less hungry and ambitious. With a smaller, more transient population, it attracts more tourists, making it harder to establish a unique identity outside of the hugely lucrative International Festival and Fringe events. It prides itself on high art, seemingly unconcerned about so-called low-brow pop music.

However, there has always been an underbelly and a sub-culture in Edinburgh that refuses to die. Despite short-sighted landlords, expensive council tax and the constant threat of closing venues, the city's underground music fraternity continues to fight on. Looking back, Auld Reekie has spawned some genre-defying scenes, ground-breaking DJs and indie trailblazers; and it continues to do so.

In the wake of the Bay City Rollers, the city's most famous and somewhat embarrassing sons, it's quite some achievement that the Fast Product and Pop Aural labels launched in the post-punk years. Bringing pioneers such as Gang Of Four and The Human League to the fore, this was the Scottish counterpoint to London's Rough Trade or Manchester's Factory Records. Local heroes Fire Engines and Scars were hardly household names but put Edinburgh on the map as part of the new aesthetic landscape of the time. Alongside the Postcard-signed Josef K, these bands are still lauded to this day and their stance has gone on to inspire many, including Franz Ferdinand, since their short, sharp existence in the early 1980s.

At the other end of the spectrum, street punks The Exploited even managed to perform on Top Of The Pops in 1981. Here's a band that even now instils devotion among its mohawk-attired followers and continues to tour the world. The chart-bothering Goodbye Mr Mackenzie followed a few years later, poised for a potential breakthrough that didn't materialise. Guitarist "Big" John Duncan played for both groups and even had a short spell as second guitarist in Nirvana. In many ways, this was one of Edinburgh's most successful periods, producing Shirley Manson, who later became a megastar in the band Garbage.

As punk and its offshoots slowly mutated, another milestone was C86 (the movement initiated by an NME cassette compilation) with The Shop Assistants briefly shining bright in a shambolic, twee-pop obsessed world, next to neighbours Jesse Garon & The Desperadoes and The Fizzbombs. When listening to current US indie-darlings such as the Vivian Girls or F***ed Up, it's not hard to feel the impact of these acts 25 years on.

The electronic scene flourished in the late 1980s and early 1990s. Now highly regarded as a tastemaker at Optimo Espacio, JD Twitch was also a key DJ and founder of the techno phenomenon that was Pure in the sadly defunct and much missed The Venue. This was a counterculture muster-point at which legendary DJs from Detroit, Chicago and Berlin performed on a weekly basis. Together with its friendly rival Sativa, Pure reshaped club culture in the capital and across the country.

Running parallel to the harder, harsher electronica was a funkier and jazzier side to the city. Hip-hop began to blossom and Sugar Bullet had a brief dalliance with success as did Blacka'nized. They both helped showcase other rappers and producers under the banner "East Coast Project", supported by the Stereo MCs and the Mo Wax label in the early 1990s. Since then, burgeoning beats labels such as Black Lantern Music and Abaga have sprung into action, delivering heavy slabs of dubstep, hip-hop and drum'n'bass online.

If Glasgow is seen as Scotland's finest indie-rock breeding ground, then Edinburgh has had its fair share of success stories too. Idlewild were Scotland's hottest property for many years, signing to the Parlophone label and making a string of superb albums in the process.

Psychedelic Fifers The Beta Band also based themselves in the capital and inspired the more recent musings of Django Django, offspring of another hotbed – Edinburgh College of Art. Indie-pop stalwarts Ballboy became John Peel's favourite band with countless releases on the ever-uncompromising SL Records; and Aberfeldy have flown the flag for well-crafted, intelligent songwriting over three splendid albums.

Ushering in a new guard of heralded songwriters today, Withered Hand, Meursault and Eagleowl all claim Edinburgh as their home and are building a fervent fanbase for their largely acoustic, alternative-folk anthems. Kid Canaveral shout the fuzz-pop odds; math-rockers Lady North astound and astonish; while electronic post-popsters Homework and Birdhead serve up a heady brew for new-music fans. This is thanks in no small way to the Song By Toad label, blog and podcast; as well as other supporters such as Avalanche Records, Radar Blog, 17 Seconds, Tidal Wave Of Indifference and Edinburgh's student radio network, Fresh Air.

Now, the tragic news hits us that The Bongo Club is set to close in the near future and Cabaret Voltaire is under new ownership. Next to a handful of others, these venues are the lifeblood of the city's grassroots culture and help forge a reputation that goes beyond the big festivals and one-off events. Edinburgh has firmly established itself artistically, across genres and styles, and will live to fight another day. But it needs local council and commercial venues to step in and help too. Or, as Song By Toad recently blogged, the city may have to trot out the dubious catchphrase "No fun please, that's what Glasgow's for!"

Vic Galloway presents on BBC Radio Scotland at 8.05-10.00pm Mondays (repeated 10pm – midnight on Fridays). He hosts a monthly gig night at Electric Circus, Edinburgh which continues on Wednesday with live music from Lady North, Homework and Birdhead. Check www.vicgalloway.com for more info.