The two firms both retained 96 per cent of the trainees they offered jobs to, while Linklaterswas 1 per cent behind.
Freshfields Bruckhaus Deringer lagged behind the rest of its peer group with a retention rate of just 88 per cent, with 37 of the 42 trainees that were offered jobs accepting a position at the firm.
Freshfields, number three in The Lawyer UK 100, has seen its retention rate fall by 6 per cent in the last three years, with the firm holding a rate of 94 per cent in 2005.
This years rate, however, is an improvement on last years figure of 85 per cent, when it dropped to its lowest level in three years.
Comparing 2005 figures to this years performance, A&O and Linklaters both managed to increase their retention rates dramatically, by 12 per cent and 10 per cent respectively.
Clifford Chance has maintained a consistent retention rate, increasing by 1 per cent on last year and its 2005 figures.
With 46 trainees qualifying in September, Freshfields had the lowest number of qualifiers and saw a drop compared with the two previous years, when 52 trainees qualified.
A&O, which is the UKs fourth highest-earning firm, also saw a drop in qualifiers, with 57 trainees completing their courses compared with 61 the previous year.
Linklaters, which along with Clifford Chance has 61 trainees qualifying this September, also saw a decrease in the number of newly qualified solicitors, with 66 gaining their qualifications last year.
A Linklaters partner said that the firms retention rate had improved vastly as the UKs number-two law firm had reduced the number of trainees it takes on.
A couple of years ago we had more than 100 trainees so it was more difficult to keep them all, explained the partner. What we have now is a smaller number of trainees but they will be among the best, which has meant that weve increased our retention rate.
He added: For all the magic circle firms, trainee retention is important as its at this grassroot level where we can ensure we get the best in this extremely competitive recruitment market.