#Real Answer
The answer is We do not know.
As far as I know, George has never talked about his inspiration behind Daenerys Targaryen, which of course we must note, there need not be any.
#Other similar historical characters
There are however a number of similar historical characters other than Cleopatra who share something with Daenerys Targaryen.
###Henry VII
There are many who draw parallels between Henry VII Tudor and Daenerys I Targaryen. The core reasons are following:
- Both of them lived in Exile across the narrow sea (Or English channel).
- Both lost their fathers in early age, Edmund and Aerys.
- Both of them are pitted against a usurper, Edward IV in Henry's case and Robert in Daenerys'.
- Another usurper appears who removes the heirs of original usurper Edward IV/Robert Baratheon. That's Richard III and Joffrey Baratheon.
- Both are the rightful heirs in eyes of some nobles.
- Both used dragons on their banners.
- Both had dissidents join them in exile.
- Daenerys had Ser Barristan, Henry had John de Vere, Earl of Oxford.
- This fits with the author's area of historical expertise. GRRM has already stated that his core inspirations come from French and English history, particularly the war of Roses.
As the Author said:
The Wars of the Roses have always fascinated me, and certainly did influence A SONG OF ICE AND FIRE, but there's really no one-for-one character-for-character correspondence. I like to use history to flavor my fantasy, to add texture and versimillitude, but simply rewriting history with the names changed has no appeal for me. I prefer to reimagine it all, and take it in new and unexpected directions.
And also:
Q: [Edited for clarity after this point. Ser Loras's (Ser Loras is the nickname of the fan) question concerning whether GRRM borrows from history, particularly Spanish history, received the reply below.]
George: Well, yes and no. I have drawn on a great many influences for these books. I do use incidents from history, yes, although I try not to do a straight one-for-one transposition of fact into fiction. I prefer to mix and match, and to add in some imaginative elements as well.
Most of my borrowings, however, come from English and French medieval history, simply because I am more familiar with those than with the heroes, legends, and traditions of other countries. The Wars of the Roses, the Crusades, and the Hundred Years War have been my biggest influences... oh, and some Scottish history as well, such as the infamous Black Dinner that inspired my own Red Wedding. This isn't a matter of choice so much as it is one of necessity. I don't have any other language besides English, and there's a paucity of good popular English language histories about medieval Spain, medieval Germany, and the like. I was in Germany last fall, and looked everywhere for good reference books about the medieval Holy Roman Empire, which would be treasure trove, I suspect. There are a ton of them that looked likely... but all in German.
And in about a week I will be travelling to Spain, coincidentally enough, where I plan to search for some good popular histories as well. Whether I will find any I can read, however... well, it's doubtful.
###Abd el Rahman I "The Eagle"
Personally, I see more of Abd el Rahman I Umayyad of Andalusia in her than Henry VII.
Here's why:
- Both were last scions of great dynasties, him the last of the Umayyads (At least he thought so at the time but later other members turned up like Aemon tried to reach Daenerys), her the last of the Targaryens.
🎶 *Oh I am the last of the Umayyads/Targaryens, my people are gone from the world. The last of the great Syrian/Westerosi Umayyads/Targaryens, who ruled half the world/Westeros at my birth.....They hunt me with dogs in the day light, they hunt me with torches by night. For these Abbasids/Baratheons who are small can never stand tall, whilst Umayyads/Targaryens still walk in the light.*🎶 - Both had their families ousted in popular rebellions.
- Both lost their father early, He lost Muawiyah, she lost Aerys.
- Both ran from their home with their brothers while their family was butchered.
- Brothers of both Abd al-Rehman and Daenerys were killed.
- Both ran for their lives, in fear.
- Both then managed to carve themselves a Kingdom with no other strength than their own.
- Both never forgot where they came from and always wanted to go back. To go East (Damascus), Abd al-Rehman had to go West (Andalus). Daenerys was told by Quaithe that to go West (Westeros) she had to go east. He wanted to go East and fate kept taking him further and further West. She wants to go West but fate keeps taking her further and further East.
- Both then decided to improve the affairs of their newly forged Kingdoms. So both of them stayed and ruled. And Abd al-Rehman planted Date Palm trees, Daenerys planted olive trees.
- Both were polyglots.
On an unrelated note, regarding the Black Dinner being the inspiration for the Red Wedding, there's sort of a Black Dinner from this character's life too. After their rival family, Abbasids deposed the Umayyads, the new Caliph Abu al-Abbas invited the members of the deposed dynasty who were still in the capital to a dinner. When the guests arrived, Abbasids had them all beaten to death with clubs before the first course. The table was set then on their corpses and Abu al-Abbas, henceforth known as As-Saffah (Blood-shedder) had dinner with his friends and Generals.
The first woman to rule the Sassanian Empire had somethings in common with Daenerys as well, although not as much as the first two candidates:
- She lost her father and most of her family when a coup in favor of her brother Kavadh II ended in wholesale murder of the Imperial Family with the King and thirty of his sons being executed by the new King.
- Kavadh died soon and Usurper Shahrbaraz a Persian General then killed his minor son Ardeshir III and claimed the throne for himself.
- While it is unknown who was her mother, It is very possible that she was a product of incest as practice of Incest was considered holy by Zoroastrianism. But if her mother was related to her father, then she'd be a proper wife, not a concubine and she would not have been unknown, as then she'd be a Persian Princess, not some random lowborn girl.
Within forty days of the usurper's actions, the loyalists murdered him and crowned Princess Pourandokht as First Sassanian female Empress. She was then deposed in favor of her sister Azarmidokht, who was then murdered by another General. So Pourandokht was crowned for a second time. And then she was murdered herself.
Yezdegerd also bears some resemblence with Daenerys:
- Both were last scions of great Dynasties. Yezdegerd was practically the last Sassanian when he was crowned.
- Both lost their fathers early. His father Prince Shahryar was executed by his uncle Kavadh II.
- In the following civil war which saw the Persian throne usurped by a General and the coronations of his aunts Pourandokht and Azarmidokht, he was hiding in Estakhr for his life.
- The rival factions however decided to make him Emperor as a compromise when he was somewhere between 12-16, when someone murdered his aunt Empress Pourandokht. A year after he was crowned, Arabs invaded and ended the Persian Empire for good. Yezdegerd fled into exile with his children.