The firm is taking on sites within branches of the Tesco-owned Dobbies Garden Centre chain in the two cities, adding to its existing portfolio of stores in Coatbridge, Inverness and Leith.
The existing aquatics section in Dundee is due to be taken over at the end of May.
In Aberdeen, construction is under way on an extension to double the size of the current department, set to open in June.
Colin Christian, regional director of Fishkeeper Scotland, said: “We have drawn up really exciting plans to hold more fish and products than ever before, stocking many of our exclusive as well as favourite species and brands, including our AquaOak aquariums.”
He added: “We are really looking forward to offering everything a fishkeeper needs in both cities and we are confident the stores will be as hugely successful as the others in Scotland.”
Christian said the stores will stock more than 200 aquariums and 5,000 exotic invertebrates and tropical freshwater, marine, coldwater and pond fish from around the world.
Fishkeeper Scotland is an independently operated arm of Maidenhead Aquatics, which was set up in 1984 and has 140 stores in England, Wales and Northern Ireland and employs more than 700 people.
Its expansion into Aberdeen and Dundee will see 12 positions retained across both sites and the firm said it expects to create up to five more jobs, taking its overall headcount north of the Border to 35.
Lasswade-based Dobbies became part of the Tesco group in 2008 after the supermarket giant tabled a £155.6 million bid for the Aim-quoted business the previous year. The move sparked a fierce tussle with Dobbies shareholder Sir Tom Hunter, who at the time also owned the rival Wyevale chain of garden centres.
According to the Ornamental Aquatic Trade Association, the UK market is worth about £400m a year.