Religion and Christianity
When the sailors first approach the island, it is only after they inform the inhabitants that they are Christians that they are allowed to land. Then, the first question they ask the Governor of the House of Strangers is how the people of the island were converted to Christianity, which delights the Governor. Christianity plays a crucial role in the development of the narrative, as it is something the strangers and the inhabitants of the island have in common. The prevalence of Christianity also suggests that it is the "true" religion, as the island is dedicated to exploration and inquiry while still maintaining their Christian values.
Knowledge
Knowledge is the governing concept behind the existence and operation of Salomon's House, the heart of Bensalem. The Father of Salomon's House explains to the narrator that knowledge lies at the foundation of their practices: they strive to acquire, synthesize, and draw conclusions about new knowledge brought to them by the Merchants of Light, who sail beyond the island every 12 years. The knowledge held at Salomon's House is described as vast, productive, and more advanced than any other civilization.
Science
Along with the theme of knowledge is that of science and the scientific method. When the Father of Salomon's House describes its structure to the narrator, he essentially outlines the Baconian method of scientific inquiry. Bacon was himself a scientist and is credited with contributing to the invention of the scientific method still used today. Part of the utopian vision of Salomon's House is the primacy placed on scientific inquiry, study, and experimentation, which leads to deeper knowledge about the universe.
Morality
Frequently throughout the narrative, the narrator and others will comment on the moral character of the people of Bensalem. Indeed, the narrator remarks that even the "meanest" (meaning humble) of residents is upstanding and righteous, committed to the society of Bensalem and the extension of generosity to strangers. This is in part what makes the narrative a utopian one, as the people who inhabit the island are congenial and caring. It also demonstrates how their Christian background has manifested in a way that aligns with the message of mercy and kindness put forth by Christ in the New Testament.
Customs and Ceremony
Customs are important to the people of Bensalem. They want to preserve their way of life so they are particular about who is allowed within their community. The sailors must submit to their requests of staying within their quarters for several days until the people allow them to wander the city. They do have restrictions of where they can go within the city, but this is for the safety of the community and the sailors. One of the customs that the crew gets to observe is the Feast of the Family, wherein a patriarch of a large family honors one of his children by asking them to live with him in his house.
Secrecy
While the narrative begins on a suspicious note – the sailors are unsure what kind of land they have encountered, and the kindness of the inhabitants is not fully realized until they are provided for in the House of Strangers – they soon learn that this secrecy is actually built into the laws of Bensalem. King Solamona wanted to keep his people safe while also avoiding some of the negative consequences that come with being involved in trade and commerce with other civilizations – things like war, slavery, etc. Thus, one of the laws of the island is that nobody (save the Merchants of Light) is allowed to leave. Strangers are permitted to return to their homes but, as the Governor of the House of Strangers informs them, few strangers have ever actually returned home, preferring the ways of life on the island to that of their own civilization.
Criticism
Inherent to most utopian narratives is an implied criticism of the world outside of the utopia. In this case, New Atlantis is subtly critical of the Europe of which Bacon himself was a part: the character of Joabin tells the narrator that while the people of Bensalem are chaste, the people of Europe have polluted Christian notions of love and marriage with money-making enterprises like brothels. In this way, the text offers a critical eye toward early modern Europe and imagines a world in which the unsavory qualities of Europe were eliminated in favor of exploration and inquiry.