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Updates: 

Update 18 to Geopolitical Entities and Codes (formerly FIPS 10-4) is dated 2014-12-31. It changes the spellings of two departments, from Atakora to Atacora and from Kouffo to Couffo.

Update 10 to Geopolitical Entities and Codes (formerly FIPS 10-4) is dated 2012-12-31. It changes the status of the divisions from provinces to departments.

I've found sources for the 2002 census data for Benin, and used them to update the populations shown here.

FIPS Publication Change Notice No. 9, affecting FIPS PUB 10-4, was issued on 2004-10-01. It assigns FIPS codes to the twelve departments, supplanting the codes for the former six provinces. They are shown in the table below.

ISO 3166-2 Newsletter Number I-2 was published on 2002-05-21. It adds the six departments created on 1999-01-15. The French Embassy published a chronology which includes these dates:
1993-01: The Estates General of the territorial administration announce a plan to increase the number of departments by dividing each of the existing ones in two (12 in place of 6).
1998-07-24: Final adoption of the five decentralization laws. The choice of the future departmental capitals will be left to the government.

Country overview: 

Short name	BENIN
ISO code	BJ
FIPS code	BN
Language	French (fr)
Time zone	+1
Capital	Porto-Novo

 

Benin began the 20th century under the name of Dahomey, as a French colony. On 1960-08-01, it became an independent member of the French Community. It has retained its borders virtually unchanged throughout the 20th century, bearing in mind that its northern (inland) borders were ill-defined in the early years.

Other names of country: 

1. Danish: Benin
2. Dutch: Benin, Republiek Benin (formal)
3. English: Republic of Benin (formal), Dahomey (obsolete)
4. Finnish: Benin
5. French: Bénin m, République f du Bénin (formal)
6. German: Benin n
7. Icelandic: Benín
8. Italian: Benin m
9. Norwegian: Benin, Republikken Benin (formal)
10. Portuguese: Benim n (m in Brazil), República f do Benim m (formal), Daomé (obsolete)
11. Russian: Республика Бенин (formal)
12. Spanish: Benín, República f Popular de Benín (formal), Dahomey (obsolete)
13. Swedish: Benin
14. Turkish: Benin Cumhuriyeti (formal)

Origin of name: 

Named for Bini, an ancient kingdom on the Gulf of Guinea

Primary subdivisions: 

Benin is divided into twelve départements (departments).

Department	HASC	ISO	FIPS	Population	Area(km.²)	Area(mi.²)	Capital
Alibori	BJ.AL	AL	BN07	521,093	25,683	9,916	Kandi ?
Atacora	BJ.AK	AK	BN08	549,417	20,459	7,899	Natitingou
Atlantique	BJ.AQ	AQ	BN09	801,683	3,233	1,248	Ouidah ?
Borgou	BJ.BO	BO	BN10	724,171	25,310	9,772	Parakou
Collines	BJ.CL	CO	BN11	535,923	13,561	5,236	Savalou ?
Couffo	BJ.CF	KO	BN12	524,586	2,404	928	Dogbo ?
Donga	BJ.DO	DO	BN13	350,062	10,691	4,128	Djougou ?
Littoral	BJ.LI	LI	BN14	665,100	79	31	Cotonou
Mono	BJ.MO	MO	BN15	360,037	1,396	539	Lokossa
Ouémé	BJ.OU	OU	BN16	730,772	2,835	1,095	Porto-Novo
Plateau	BJ.PL	PL	BN17	407,116	1,865	720	Sakété ?
Zou	BJ.ZO	ZO	BN18	599,954	5,106	1,971	Abomey
12 departments				6,769,914	112,622	43,484
HASC: Hierarchical administrative subdivision codes. ISO: Department codes from ISO 3166-2. For full identification in a global context, prefix "BJ-" to the code (ex: BJ-LI represents Littoral). FIPS: Codes from FIPS PUB 10-4. Population: 2002-02-11 census (source [1]). Area: Data provided by Jose Gavinha. Capital: The capitals of six departments have not yet been designated. Jose Gavinha reports that the cities with question marks have begun providing department-level government services.

Further subdivisions:

See the Communes of Benin page.

Benin now consists of twelve départements (departments), subdivided into 77 communes, which in turn are divided into arrondissements and finally into villages or city districts. Before the reorganization of 1999, it had six provinces, further divided into 84 districts, which were categorized as urban or rural. Before independence, the six provinces were subdivided into 29 préfectures.

Territorial extent: 

The UN LOCODE page  for Benin lists locations in the country, some of them with their latitudes and longitudes, some with their ISO 3166-2 codes for their subdivisions. This information can be put together to approximate the territorial extent of subdivisions.

Origins of names: 

1. Atacora: from Atacora mountain range
2. Atlantique: from Atlantic Ocean
3. Collines: French for hills
4. Littoral: French for coast

Change history: 

1. 1904: French colony of Dahomey incorporated into French West Africa as a territory.
2. 1920: In the aftermath of World War I, the former German colony of Togo was split from north to south. The western third was mandated to Great Britain, and the eastern two-thirds to France. For part of the period between the wars, Dahomey and the French mandate of Togo were combined under the name Dahomey for administrative purposes.
3. ~1923: Capital moved from Abomey to Porto-Novo.
4. 1975-11-30: Country name changed from Dahomey to People's Republic of Benin. These were the provinces of Benin at that time.

Province	ISO	FIPS	Population	Area(km.²)	Area(mi.²)	Capital
Atacora	AK	BN01	479,604	31,200	12,046	Natitingou
Atlantique	AQ	BN02	686,258	3,220	1,236	Cotonou
Borgou	BO	BN03	490,669	51,000	19,691	Parakou
Mono	MO	BN04	477,378	3,800	1,467	Lokossa
Ouémé	OU	BN05	626,868	4,700	1,815	Porto-Novo
Zou	ZO	BN06	570,433	18,700	7,220	Abomey
6 provinces			3,338,240	112,622	43,484
ISO: Codes from ISO 3166-2. FIPS: Codes from FIPS PUB 10-4. Population: 1979-03-20 census (source [3]).

1. 1999-01-15: Alibori department split from Borgou; Collines department split from Zou; Couffo department split from Mono; Donga department split from Atacora; Littoral department split from Atlantique; Plateau department split from Ouémé. The divisions were sometimes called departments before this date, but the designation seems to have changed officially at this time.

Other names of subdivisions: 

1. Alibori: Département de l'Alibori (formal)
2. Atacora: Atakora (variant); Département de l'Atacora (formal); Nord-Ouest (obsolete)
3. Atlantique: Département de l'Atlantique (formal); Sud (obsolete)
4. Borgou: Département du Borgou (formal); Nord-Est (obsolete)
5. Collines: Département des Collines (formal)
6. Couffo: Département du Couffo (formal); Kouffo (variant)
7. Donga: Département de la Donga (formal)
8. Littoral: Département du Littoral (formal)
9. Mono: Département du Mono (formal); Sud-Ouest (obsolete)
10. Ouémé: Département de l'Ouémé (formal); Sud-Est (obsolete)
11. Plateau: Département du Plateau (formal)
12. Zou: Centre (obsolete); Département du Zou (formal)

Population history:

Source is [1]. Presumably, figures for the first two censuses were found by totaling the populations of communes that belong to those departments in the present configuration; six of the departments didn't exist until 1999.

Department	1979-03-20	1992-02-15	2002-02-11
Alibori	213,078	355,950	521,093
Atacora	294,629	400,613	549,417
Atlantique	365,910	529,546	801,683
Borgou	277,591	471,975	724,171
Collines	217,075	340,284	535,923
Couffo	273,536	395,132	524,586
Donga	184,975	248,695	350,062
Littoral	203,842	536,827	665,100
Mono	320,348	281,245	360,037
Ouémé	418,146	568,898	730,772
Plateau	208,722	307,676	407,116
Zou	353,358	478,714	599,954
Total	3,331,210	4,915,555	6,769,914

Sources: 

1. [1] "Synthèse des Résultats , Troisième Recensement General de la Population et de l’Habitation", INSAE, Cotonou 2003. Page 13 has populations by department from the three censuses.
2. [2] Afrikinfo  has a summary of the 1992 census results. This was the first source I found for those figures. It uses the pre-1999 divisions. I tried to calculate the populations of the new departments by summing the populations of their constituent communes. In doing so, I found that about six of the commune populations had an incorrect digit, but couldn't tell which communes or which digit.
3. [3] "The Statesman's Year-Book 1988-1989", John Paxton (ed.). St. Martin's Press, New York, 1988. Some of these figures are inconsistent with source [1]. Specifically, the total population is 7,030 too high (by comparison with the total of the individual department figures), and 116,506 people were transferred from Mono to Atlantique (by comparison with source [1]).