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Aylmer on record (, life of Aylmer, pp. 8–10.

On the accession of Elizabeth he returned to England, and was appointed one of eight divines to hold a disputation at Westminster with a corresponding number of the Roman Catholic persuasion. In 1562, through the influence of one of his pupils abroad (Thomas Dannet) with Cecil, he was promoted to the valuable archdeaconry of Lincoln. For the next fourteen years he resided in that city, attending to the affairs of the diocese, and occasionally assisting Archbishop Parker in his efforts on behalf of learning by researches in the cathedral library. He sat in convocation in 1562, and subscribed to the Thirty-nine Articles. In 1573 he received by accumulation the degrees of B.D. and D.D. at Oxford.

On 24 March, 1576–7, Aylmer was consecrated bishop of London in succession to Sandys, and from this time his arbitrary and unconciliatory disposition comes frequently into unpleasing prominence. He quarrelled with his predecessor (a man like himself of hot temper) respecting their relative claims to the revenues of the bishopric, and again on the question of dilapidations. His rule of his diocese was characterised by exceptional severity, fines and sentences of imprisonment being frequently imposed on those who differed from him on doctrinal questions, whether puritans or catholics. A young bookseller who had sold a copy of the celebrated 'Admonition to Parliament,' a work attributed to Cartwright, in which the episcopal office in the abstract and the actual holders of it in the English church were alike unsparingly criticised, was also committed by him to prison. He used his best endeavours to crush the recently revived university press at Cambridge (State Papers, Domestic, Eliz. clxi. l). The unpopularity which he evoked by these and similar measures is indicated by an information which was laid against him about this time for having felled all the elms at Fulham, a charge which Strype denounces as a 'shameful untruth.' Aylmer appears, however, to have become conscious that his opportunities for usefulness in his diocese were to a great degree lost, and made more than one unsuccessful attempt to obtain his removal to a less laborious see, to Ely or Winchester. Whitgift, who appears to have approved his policy in general, appointed him to preach before the queen on her birthday in 1583; but Aylmer having shortly after ventured to obtain the royal warrant for committing Cartwright, the great puritan leader, to prison, Elizabeth, with her habitual disingenuousness, deeming it prudent to disavow the proceedings, manifested signs of her displeasure. His enemies, who were not few, endeavoured to avail themselves of this circumstance by bringing forward charges against him of misappropriation of the episcopal revenues, an accusation which he appears to have successfully repelled by furnishing Burghley with a detailed account of his financial position and that of the see. In the same year, when on a visitation in Essex, he only escaped a public insult in Maldon Church through having been apprised of the design beforehand. Having learned the names of the instigators, he showed his usual resentful temper by sending them to prison. It is not surprising to find that when, in 1588, the Martin Marprelate tracts appeared, Aylmer was singled out for their fiercest satire. The closing years of his life showed, however, no softening in his policy. He took a leading part in the deprivation of Robert Cawdrey, a clergyman at Luffenham, for some injudicious remarks respecting the prayer-book — a measure that resulted in four years of irritating litigation. He also suspended, on like grounds, 'silver-tongued Smith,' a young and able divine, and the most popular preacher of the day; and again (much against the wish and advice of Burghley) Robert Dyke, of St. Albans.

Elizabeth appears to have been desirous of seconding Aylmer's wish to be removed to another see, and suggested that of Worcester, and Bancroft as his successor in London. Negotiations with this view were accordingly commenced, but Aylmer's impracticability of temper led him to insist on conditions which Bancroft would not accede to, and after three ineftectual endeavours to arrive at an understanding the latter abstained from all further discussion on the subject. Shortly before his death, however (3 June, 1594), Aylmer expressly intimated his hope that Bancroft might succeed him (MSS. Baker, xxxvi. 335).

He was interred in St. Paul's Cathedral, but the 'fair stone of grey marble' which marked the place of his interment no longer appears. The inscription, which was altogether free from fulsome eulogy, sententiously recorded that he

Ter senos annos Præsul; semel Exul, et idem Bis Pugil in causa religionis erat.

He married Judith Bures, a lady of Suffolk, by whom he had seven sons and three daughters. Of the former, one (Samuel) was sheriff for the county of Suffolk; another (John) was knighted, and resided at