|Sir Francis Bryan by Hans Holbien|
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What does this source tell us about Sir Francis Bryan #1 and his possible relationship to the father of Sir Francis Bryan of Ireland? Not much, it confirms that Sir Francis had a son, but he was illegitimate and unnamed.
Old Journal articles: Unpublished Geraldine Documents: The Earls of Desmond 
Stratham, September 16th. - Selve received three days ago the dispatch that the admiral sent to him by the son of Sir Francis Bryan, who arrived safe and sound with and except with oneLesson learned, never overlook books in other languages! What this particular books tells us is that Sir Francis appears to have had a grown son, unnamed by Odet in 1548. He would likely to have been at least 21, so he could not have been a son of
of thepeople of Selve in London, from where he departedto go find his father. Earl of Bryant has for a short time been marrying an Irish citizen named the Comtesse de Ouarmontand is going to Ireland to partyto see the good of his wife, but chiefly as I am sorry for the affairs of this king.
This will is written in English, but 17th century script is difficult to decipher, it's fun to try though, like putting a puzzle together. Margaret outlived all her children. She does not mention any grandchildren, not even a poor son of Francis.
A Wee bit O' Irish History
According to the story of WSB his father was Sir Francis Bryan #2. I have been unable to find any proof that this man was the son of Sir Francis #1, but that doesn't mean that he didn't exist. Let's look a litter closer at his story. According to his profile on both Wikitree and Geni, he was born in 1549 in County Clare in Ireland. Both websites agree he died in County Clare in 1640. Before I go on I have to same something about all these dates for births and deaths in the Bryan family. Did you notice, as I did, that everyone is born and dies on the 1st of June? This is a bright red flag that tells me someone is 'making this shit up', pardon my French.
Anyway, back to County Clare. Sir Francis #1 lived with his reluctant wife in Clonmel in Tipperary in the Province of Munster, a seat of power of the Earls of Ormond. Joan Fitzgerald's first husband was James Butler, 9th Earl of Ormond and her son Piers was his heir. After the death of Sir Francis, Joan married her powerful cousin, Gerald Fitzgerald, the 15th Earl of Desmond. The Desmond family also controlled a huge swath of Munster. Joan's father was the 10th Earl of Desmond. Joan's life was firmly planted int the Desmond/Ormond lands of her father and her son.
County Clare, despite it's Norman name, was part of the Kingdom of Thomond and home to the powerful Irish family the O'Briens. No child of Sir Francis Bryan #1 would have been born in County Clare. He would not have inherited land in County Clare as his mother would not have inherited land in what was if not enemy territory certainly adversarial.
According to his bio Francis father of WSB was a knight. This claim should be pretty easy to sort out. I reference a set of book called The knights of England
Land Owners of County Clare  
From the story of WSB we are told that he was a land holder in County Clare. He married Catherine Morgan and had a large family at the time of Cromwell's invasion in 1641. County Clare has an amazing library which has a significant amount of content available online. One of the database which is searchable is the Book of Forfeitures and Distributions. Here is an explanation of this database:
The Books of Survey and Distribution were compiled by the English government at the end of the 17th century to establish a reliable record of landowners in Ireland for the purpose of imposing rent (the Quit Rent). The Books incorporate information collected during earlier surveys – the Strafford, Civil and Down Surveys – detailing the names of proprietors who forfeited their land under the Cromwellian Settlement of 1641 and the amount and quality of land they held. The names of those to whom this land was granted, under various Acts between 1662 and 1703, is also given.Guess whose name is not found on this survey of land owners whose lands were confiscated by Cromwell. There is no Sir Francis Bryan and there is no William Smith Bryan or just plain William Bryan. If WSB held extensive land in County Clare in 1641 his name would be on this survey.
There is also a book called The Irish And Anglo-Irish Landed Gentry, When Cromwell Came to Ireland: Or, a Supplement to Irish Pedigrees. Surely if WSB held land in Ireland which he lost when Cromwell busted him to Virginia, his name would appear somewhere in the 792 pages of this books, alas he is not to be found.
No WSB can be found on The Down Survey for Ireland., nor is he mentioned in the 1641 Depositions.
Reclaiming forfeited land 
Francis Bryan, son of WSB returned to Ireland to reclaim his fathers hereditary titles and lands. So far we have seen no such land but there are books and data on those who did make a claim to recover their confiscated estates. There is a book aptly named Lists of the Claims as they are Entered With the Trustees at Chichester House on College Green Dublin On or Before the 10th of August 1700. This is a list of over 3100 claimants to lost land. There is no William Smith or Francis Bryan on this list.
What's the big deal with Denmark?
WSB married Catherine Morgan in Denmark. Why? What was he doing in Denmark, what was she doing in Denmark? This is so weird.
Francis Bryan #3, son of WSB goes to Ireland to reclaim his father's land. Somehow he ends up in Denmark where he marries Sarah Brinker. FB#3 dies in Belfast? Does no one else think this is crazy?
I think the Denmark references are an attempt to make a connection to Morgan Bryan whose grandfather was Danish as per his son's American Revolution Pension Application.
WSB in Virginia
So, WSB is sent by Cromwell to Virginia. The Prince of Ireland is dropped off and that's it. No record of this man in Virginia exists. Why? I believe it's because he did not exist in the first place.
 London Metropolitan Archives and Guildhall Library Manuscripts Section, Clerkenwell, London, England; Reference Number: MS 9172/2A; Will Number: 49
 John Kennedy, A History of the Parish of Leyton, Essex, (London: Phelp Brothers, 1894) p.344; transcription of her will.
 William Arthur Shaw,
 James Frost, The History and Topography of County Clare, (Dublin: Sealy, Byers and Walker, 1893.
 John O'Hart, The Irish And Anglo-Irish Landed Gentry, When Cromwell Came to Ireland: Or, a Supplement to Irish Pedigrees,(Dublin: James Duffy, 1892).
 Great Britain. Trustees for the Sale of the Forfeited Estates in Ireland, Patrick Campbell, and Joseph Ray. A List of the Claims As They Are Entred With the Trustees: At Chichester-House On College-Green Dublin, On Or Before the Tenth of August, 1700. Dublin:: Printed by Joseph Ray, and are to be sold by, 1701.