Flintshire on Wikipedia.

Alltami, Bryn Methodist Church. SJ 266 655. © Mike Berrell (2009).

Bagillt.
Broughton, the former Primitive Methodist Chapel. © Gerard Charmley (2010).
Brynford, St. Michael. © Martin Briscoe. Another view, and the adjacent building - possibly a Sunday School, both © Carl Hogan (2014). The church also featured in the Unknown section - Leslie was trying to identify a church with family associations. The family lived near Duckington in Cheshire from about 1873-82, and in Eccleshall, Staffordshire until about 1890. However the church, identified by Jay Priest, proved to be Brynford Church. The first photo here clinches it. The former Saron Chapel (Calvinistic Methodist), now in secular use. © Carl Hogan (2014).
Buckley.

Caelcoed, Methodist Chapel. © Carl Hogan (2015).
Caerwys, the former Seion Baptist Chapel (1891) on South Street, now in secular use. © Carl Hogan.
Carmel, Capel Seion yr Annibynwyr. Presbyterian Church. Both © Martin Briscoe.
Connah's Quay, St. John's Methodist Church on High Street. Originally Methodist New Connexion (1883). © Chris Emms (2010).

Dolphin, the former (and very derelict) Ebenezer Wesleyan Baptist Chapel on Milwr Road. © Carl Hogan (2014).

Ffynnongroyw.
Flint.
Flint Mountain, St. Thomas (CiW, 1875). Bethel Welsh Wesleyan Methodist Chapel. Both © Carl Hogan (2014).

Garden City, St. Andrew (CiW). U.R.C., originally Congregational). Both © Gervase N. E. Charmley (2010).
Gorsedd, St. Paul (CiW, consecrated 1853). SJ 152 766. © Martin Briscoe. Another view, © Carl Hogan (2014).
Greenfield, Holy Trinity (18701) on Basingwerk Avenue. SJ 194 776. Grade II listed. The former Alpha Chapel (Congregational) on Greenfield Road has been converted into flats. SJ 194 776. Both © Carl Hogan (2014).
Gronant, St. Winifred (CiW) on Nant y Crai Lane. SJ 093 831. Bethel yr Eglwys Fethodistaidd (1869) on Gronant Hill. SJ 092 833. Talacre Abbey on Abbey Drive, formerly an enclosed order of Benedictine nuns, and now a private residence. SJ 104 833. All © Mike Berrell.
Gwaenysgor, St. Mary. SJ 075 810. Link. Rehoboth Chapel. Judging by the lack of signs, this may have been converted to domestic use. Can you confirm? SJ 074 810. Both © Steve Bulman.
Gwespyr, Capel Gwespyr (Methodist, 1860) on Tanrallt Road, now in secular use. The chapel sign. SJ 115 835. Wesley's Memorial Chapel on Tanrallt Road, also now in secular use. SJ 115 835. All © Carl Hogan.

Halkyn, St. Mary. Interior view. Both © Tim Hollinghurst. Link.
Hawarden, St. Deiniol. From an old postcard in Steve Bulman's Collection. The South Chapel (interior view, window) contains a monument to W. E. Gladstone, who died at Hawarden, though he is buried at Westminster Abbey; all © Kenneth Paver (2012). Previously in the "Unknown" section, this old photo from John Bowdler's collection shows St. Deiniol's Library; the church is at the right hand edge. Identified by Bill Davison. Link.
Higher Kinnerton, All Saints. © Jane Marriott.
Holywell.
Hope, St. Cynfarch. © Jane Marriott.

Llanasa, St. Asaph and St. Cynderyn. SJ 107 814. © Mike Berrell. Three further views, all © Steve Bulman - 1, 2, 3. Link. Former chapel, now in secular use. SJ 110 821. © Mike Berrell. Janet Gimber advises that this was Ebenezer Wesleyan Methodist.
Llan-eurgain, St Eurgain and St. Peter. Interior view. Both © Tim Hollinghurst. Link. U.R.C., © Carl Hogan (2014).
LLoc, Sion Chapel. This is named as Wesleyan Meth. on the 1894 map, and as Mount Zion on a list of Methodist churches and chapels in 1940. SJ 137 770. © Carl Hogan (2010). Link (scroll to the bottom). Coflein entry.The former Penygelli Welsh Baptist Chapel, now in residential use. SJ 139 769. © Carl Hogan (2014).

Mold.
Mostyn.

New Brighton, St. James. To the right is what looks like a tin chapel. Can you confirm? SJ 254 654. © Mike Berrell (2009). From the examination of old maps, Howard Richter suspects that this has never been a church, and always seems to have been the church hall it is today. Former Wesleyan Methodist Chapel, now in secular use. SJ 253 654. © Mike Berrell (2009).
Northop - see Llan-eurgain.

Oakenholt, Flint, Flintshire - see Flint.

Pantasaph, St. David (R.C.). © Martin Briscoe. Another view. © Carl Hogan (2010).
Pen-y-Ffordd, Gwynfa Chapel (Presbyterian Church of Wales, 1805) on Rhewl Fawr Road. SJ 135 815. The former Peniel Capel Wesleyaidd (Wesleyan Methodist, 1899) on Rhewl Fawr Road, now in secular use. SJ 135 815. Next door stands the former Peniel Chapel (1921), now also in secular use. Can you advise the denomination? All © Carl Hogan. My appreciation to Janet Gimber, who has advised that both Peniel chapels were Wesleyan Methodist, the larger one succeeding the older. The 1899 chapel then became the church hall, and was probably used as a Sunday School.
Penmynydd, St. John the Baptist. Penmynydd has absorbed the tiny village of Pentrobin, though the church board still says Pentrobin. © Jane Marriott.
Pentre Halkyn, Salem Methodist Chapel, built as Wesleyan in 1896. © Carl Hogan (2014). Link.
Pentrobin - see Penmynydd.

Queensferry, the former Bethel Calvinistic Methodist Chapel (for sale in 2010). The former Primitive Methodist Chapel partially visible behind shops. Church of the Blessed Trinity (R.C.), originally Methodist. All © Gervase N. E. Charmley (2010).

Rhosesmor, St. Paul (CiW). © Gerard Charmley (2010). Link.

Saltney. This suburb of Chester straddles the Flintshire border, and the Flintshire churches are listed under Chester.
Sandycroft, St, Francis. Methodist Church (1861). Both © Gervase N. E. Charmley (2010).
Sealand, St. Bartholomew. © Gervase N. E. Charmley (2010). Link.

Talacre, Methodist Church. SJ 123 847. © Mike Berrell.
Trelawnyd, St. Michael. Another view. There is a churchyard cross, which (according to Pevsner) is 14th century. Another view. SJ 088 796. Link. Ebenezer Chapel has dates 1701 and 1908 on the wall plaque. SJ 091 798. Nasareth Chapel (Welsh Presbyterian). SJ 091 797. All © Steve Bulman.
Trelogan, the former Disgwylfa Methodist Chapel (Calvinistic Methodist, 1826, re-built 1868), now in secular use. SJ 117 800. The former Mynydd Seion Welsh Wesleyan Methodist Chapel (1899), also now in secular use. SJ 117 802. The former Sarn Welsh Independent Chapel (1823) Became Congregational. SJ 115 790. All © Carl Hogan (2014).

 

Whitford, St. Beuno and St. Mary. Another view. Both  © Martin Briscoe.