Production of the Martin 0045S (2002, SPECIAL EDITION) began in 2002 and ended in 2004. It was a Martin Custom Shop limited edition (only 50 were made) using a design based on the 1902 prototype that eventually became the Martin style 45. This model has an unusal butterfly shaped tortoisehell pickguard decorated with mother-of-pearl and inlaid into the top between the soundhole and bridge. The fingerboard inlays are ornate abalone tree of life style with abalone inlays around the edge of the soundboard.

The ALTERNATIVE II 000C (2002, SPECIAL EDITION) was made between 2002 and 2003

The Martin ALternative II Resonator was the resonator-cone version of the Alternative II and was introduced in 2003 as a special edition. This unique 000 round neck cutaway is the first resonator guitar ever offered by C. F. Martin & Co. Designed for the person who wants the resophonic sound, both acoustically and plugged in. It is untraditional in the sense that it is constructed with a unique shallow soundwell and incorporates a traditional braced acoustic guitar back.

Production of the ALTERNATIVE III DC (2002, SPECIAL EDITION) began in 2002 and ended in 2003

The CEO'S CHOICE CEO-3 (1999, SPECIAL EDITION) was made between 1999 and 2000

Made from 2002 to 2004, the Martin CEO-5 was a special edition D-12 style dreadnought with bearclaw Sitka spruce top. Both bridge and fingerboard were striped ebony. Martin CEO C.F. Martin IV asked the Acoustic Guitar Magazine Discussion Group for their design ideas and the resulting guitar was named as the CEO's choice.  The interior paper label was signed by C.F. Martin IV. The peghead was slotted and faced with East Indian rosewood with a small raised gold foil logo.

MARTIN made the CERTIFIED SWD RED BIRCH (2003, SPECIAL EDITION) between 2003 and 2004

The CERTIFIED WOOD SWD (1998, SPECIAL EDITION) was made between 1998 and 2000

MARTIN produced the CONCEPT II (1999, SPECIAL EDITION) between 1999 and 2000

Production of the CONCEPT J CUTAWAY (1998, SPECIAL EDITION) began in 1998 and ended in 1999

The Martin D-18 Golden Era model is based on the D-18 from Martin's golden era (1930-1940).

The Martin D-45GE GOLDEN ERA (2001, SPECIAL EDITION) was made in limited numbers between 2001 and 2004 and is based on the 1937 Martin D-45. It has many features in common with the 1937 D-45 including: Adirondack spruce top with scalloped 5/16" Adirondack braces, forward shifted X, select Brazilian rosewood back and sides, linen reinforcing strips, ivoroid binding, highly colored Paua abalone trim and rosette.  The inside label is signed by C.F.Martin IV.

The Martin D-18 GE (Golden Era) 1999 Special Edition was based on the 1934 D-18, and since then the D-18 Golden Era models have had the same 1934 specifications.

MARTIN introduced the D28-GE GOLDEN ERA special edition in 1999. It was a Martin Custom Shop reissue of the pre-war Martin D-28 herringbone using Martin's precious stocks of Brazilian rosewood for the back and sides. This model continued as a special edition until the pre-CITES Brazilian rosewood supplies ran out around 2005. The original list price was $9,999 (Martins most expensive guitar at the time). The top bracing was DOM forward shifted using solid Adirondack Spruce/ scalloped 5/16'' Golden Era braces.

Martin introduced the DC-AURA Custom Shop Limited Edition in 2004. It had the Fishman "Aura" System electronics, full gloss lacquer finish and enhanced appointments including Style 41 top inlay, hexagon outline fingerboard inlays, and C. F. Martin script logo in mother of pearl on the headplate.

According to Martin Guitars: A Technical Reference, Book 2. By Richard Johnston, Dick Boak, Mike Longworth, the EMP-NS employee model was the Night Shift employees model, maple/spruce 14-fret Dreadnought with M&T neck joint. Black binding, transparent gloss black finish on maple, natural top, satin black on neck. Ebony bridge and fretboard with style 18 abalone dots, black pickguard and chrome tuners. List price $2299. 73 were sold and there was 1 prototype.

Production of the GRAPHITE II (2003, SPECIAL EDITION) began in 2003 and ended in 2004

MARTIN produced the OM-28 GOLDEN ERA (2003, SPECIAL EDITION) between 2003 and 2004

The Martin OM-28 Marquis (Special Edition) was introduced in 2005 - with approximately 100 made in total. It has simple pre-war Golden Era styling and a 1.75" wide neck that makes it ideal for finger style players. Other features include: double bound 000 body with an Adirondack spruce top, forward-shifted X-braces and select Indian Rosewood for the sides, back and head plate. The mahogany neck has a soft V profile joining the body at the 14th fret. The ebony fretboard has abalone slotted diamond inlays and 20 frets.

MARTIN manufactured the SWB (1999, SPECIAL EDITION) between 1999 and 2000

The SWC (1999, SPECIAL EDITION) was made between 1999 and 2000

MARTIN produced the WOODY GUTHRIE 000-18 WG (1999, SPECIAL EDITION) between 1999 and 2000