Well, this depends on:
Do you mean AFRICAN (Morocco to Cape including Egypt)?, or Afrotropical? Do you include Madagascar? Mauritius?
If you include the strictly geographical continent, it's tricky because of the mediterranean species and adventives.
If you would be happy with the usual pragmatically bio-geographical (ie Ethiopa down to Chad and across subsharan west africa, down to southern cape and madagascar, and the islands south of the Canaries), it's probably "a bit easier".
Thread #1261 has 4 pages of useful rare taxons info
here.
NB.
There are yet-to-be-determinined final decisions to resolve some taxons in particular species-groups, particularly among the Graphiums and also the
P. nireus group (eg
thuraui / occidua / heathi / cyclopis / viphya, and whether
nireus nireus, n. lyaeus, and
n. pseudonireus represent species complexes, and whether
P chitondensis, and also some island nireus group taxons, are all
bonae species or not).
Then there are the Graphiums in groups listed below, some are virtually unkown.
And the policenes group with a couple of less often seen taxons.
Presently, there are generally thought to be 90-100 species, and many more subspecies besides.
Combined nDNA and mtDNA studies in the future may yet have a large influence in resolving some difficult taxons.
The Rarest.
1. Well, there are those species less often seen in collections, because of difficult accessibility or seasonal barriers. Or very small habitat area;
2. Then those whose females are genuinely difficult to find even in the areas where males are not especially infrequent (if you know how to find those);
3. And those taxons where neither males nor females are encountered except very very occasionally in a century.
Here's a list I would offer, YMMV.
Rarest of all:
G. abri I only know of the original two type specimens - AFAIK this is still the case.
G. aurivilliusi known by a very few specimens from 19th century. Any from 20th? I have no information about any recent re-discoveries.
Thereafter:
Rarest in collections: mostly in Genus
Graphium.
Note that very little is known about many of these, including lifecycle (or foodplants for certain).
G. olbrechtsi - is it a
bona species?? Virtually nothing known about it.
G. junodi - occasionally seen in old or specialist collections.
G. policenoides
G. flavisparsus (
bona species?)
G. schaffgotschi (Angolanus group: Angola, Namibia, a bit of southern DRC, and a bit of W Zambia)
G. levassori (Comores Is.)
&
G. poggianus; kigoma (
bona species??);
deliae (Libert & Collins 2007);
simoniPapilio arnoldiana (Ethiopia) - never seen one, only photographs.
Papilio chitondensis (
nireus group)- recently rediscovered in a specific difficult plateau locality in Angola by Thierry Bouyer, only 12 specimens incl [
four]
2 females returned. All in specialist collections.
Papilio ufipa - only exists in Ufipa plateau in Tanzania, but I've never seen a female, occasionally males (though as often fakes usu.
P. desmondi sspp.) appear in the various marketplaces.
Then,
Any of the Island species (includes some debatable species taxons vs. ssp., eg
P. nerminae),
P. manlius (from Mauritius, in
nireus group), and
G. levassori listed above, are scarce in collections, for obvious limitations re habitat & political / expeditionary reasons.
P. zalmoxis females (probably less often captured than the also rare antimachus females).
G. gudenusi females (I was led to believe that for a long time Steve Collins had the only one known).
G. auriger females, and any other females in that group of central african
ucalegon / odin/ simoni/ olbrechtsi / deliae (Libert & Collins 2007 - Zambia endemic) /
aurivilliusi / rileyi / poggianus / [
kigoma if
bona species] /
abri etc etc group.
G. leucotaenia especially females (habitat loss and high flight path).
Not sure whether this helps?