Besides the very apparent change in the nose outline, several other important details of the fuselage construction have been modified during the life span of the Spitfire Mk. IX/XVI. The most important external differences are reviewed below.
Early Mk. IXs had short carburettor intakes (shorter and significantly chunkier than the Mk. V). During 1944 the long Vokes Aero-Vee filter unit became more or less standard, both in production and as retrofits. This unit was from the outset intended as standard on the Mk. VIII which mainly went to tropical theatres, but the planned move of numerous Spitfire Mk. IX-equipped squadrons into primitive airstrips on the continent following D-day justified this modification to all aircraft. The introduction of the air filter necessitated reposition of the external starter battery socket from the lower nose cowl to the starboard cowling panel.

The
Spitfire serving as a backdrop for this cheery portrait of the pilots of No.
302 (Polish) Squadron shows the early type carburettor intake, here also
equipped with ice guard. Note also the straight tapered cannon barrel
fairing, characteristic of the c-wing armament.

A
mid-production Spitfire LF Mk. IX shows the long
carburettor intake. Its fairing housed the integrated Aero-Vee air filter which
rendered the previous add-on tropical filters of the Spitfire Mk. V
unnecessary.
[Crown Copyright]
Similarly to previous photo-reconnaissance versions of the Spitfire, the lower engine cowling was significantly deeper on the PR Mk. XI to accommodate the larger oil tank necessitated by the long PR flights.

Post-war Danish PR Mk. XI showing the deeper profile of the lower engine
cowling which was characteristic of this version
[Danmarks Flymuseum]
During the first years of Spitfire production, from Mk. I through Mk. IX, the rear fuselage skins were attached using round-headed rivets. This applied to the area aft of the cockpit - beginning just aft of the cockpit entry door. Flush riveting was introduced at some point - probably differing between the various production lines. For the Mk.IX, it seems that it was introduced with Castle Bromwich-produced airframes in the first half of 1943, It can be seen on airframes in the MA serial range onwards but might also apply to the LZ-serialled machines built on the same order.

These two photos show the change of fuselage riveting which occurred in the middle of Spitfire Mk. IX production run. Pop rivets are evident in the above photo, starting with the fuselage frame behind the cockpit and extending all the way to the tail. The lower photo of the later-production Mk. IX fuselage shows the same area completely smooth.
[Martin Waligorski]

As is widely known, late Spitfires Mk. XVI and a few very late Mk. IXs had the cut-down rear fuselage and teardrop hood seen on other late-mark Spitfires.

Cut-down rear fuselage and enlarged rudder of the late-series LF Mk. XVI.
[Martin Waligorski]
The I.D. light on the fuselage spine, aft of the antenna mast, was deleted during Mk.IX production. It is not seen on machines from the MA serial range and onwards.
The earliest operational Mk. IXs had the Mk. V-type IFF wire antennae stretching from both sides of the fuselage (just behind the radio hatch on the port side ) to the tips of the horizontal stabilizers. Later machines had a narrow antenna mast under the starboard wing just in front of the aileron. The change seems to have occurred at about the same time as the elevator balance horn modification described above. However, the isolator at the "clothesline" I.F.F. aerial exit point remained in Spitfires produced long after this aerial had been deleted.
Most machines were equipped with a chute for signal flares in the rear fuselage, exiting at the starboard side of the spine just in front of the starboard rear access hatch. This opening was regularly taped over, like the gun ports. I do believe that some late machines lacked this chute.

Another view of FY-V of
No. 611 Squadron shows many of the fuselage details described herein. The
IFF antenna is a wire spun between the fuselage and the horizontal tail -
it's attachment point is seen as a spot on the white circle of the roundel.
Also, the I.D. light is still located at the fuselage spine behind the
antenna mast.
Well visible is also the large cannon blister characteristic of the early
production c-type wing.
[Crown Copyright]