He was a small, late foal, born in May and was never entered in the Classics as he was thought unlikely to be strong or mature enough to compete at the highest level at an early age.

[3] Rose thought so highly of Cyllene that he arranged a "luxurious" private train to ensure that the colt returned to Newmarket promptly after his races.

[6] He was then sent to Ascot for the Triennial Stakes where he defeated Nun Nicer, a filly who won the following year's 1000 Guineas, establishing himself as one of the best of an apparently "above the average"[7] generation.

At Sandown in July he won the National Breeders' Produce Stakes by a head to take one of the season's most valuable two-year-old prizes, despite being unable to obtain a clear run until the closing stages.

[12] In September he produced his best performance to date to win the Jockey Club Stakes at Newmarket by six lengths from a field which included Dieudonne and the Classic winners Airs and Graces and Chelandry.

[15] According to one correspondent, Cyllene "simply played" with the top quality field, with his jockey Sam Loates having time to stroke the horse's neck and touch his cap to the cheering crowd in the closing stages.

[16] The effects two races on firm ground[17] meant that Cyllene's connections abandoned plans to run him for a third time at the meeting (in the Hardwicke Stakes)[18] and the colt was given an extended rest.

In autumn there was much anticipation of a meeting between Cyllene and the Triple Crown winner Flying Fox,[19] with Charles Day Rose being reported as saying that he "looked forward to beating" the outstanding three-year-old in the Champion Stakes at Newmarket.

[24] In June 1899, shortly before his runs at Royal Ascot, Cyllene was rated by the Daily Mail's correspondent as one of the three best horses in England, alongside the Australian-bred Newhaven and the three-year-old Flying Fox.