Love
The principal theme of the novella is love, and the winning of it. The key plotlines all revolve around love; Pyrocles decides to dress up as a woman because he has fallen instantly in love with Philoclea. Midorus decides to dress up as a shepherd because he has fallen in love with Pamela. Gynecia is in love with the man she supposes Cleophila is underneath the disguise. Basilius falls in love with the woman he is disguised as. Mopsa is in love with Dorus and he pretends to be in love with her so that he can woo Pamela uninterrupted by her guardians. The nature of love is also shown in a number of different ways that become sub-themes; unrequited love, jealous love, equality in love. All of these things are branches from the original theme of love.
Unrequited Love
Unrequited love is a popular theme in Medieval literature and this novella is no exception. It is also the love that causes the most jealousy and problems for the people invested in it. In this case, Gynecia is suffering from the unrequited love she feels for Cleophila/Pyrocles and this suffering causes her to temporarily lose her mind and not only try to cheat on her husband with Cleophila but also to kill her/him when it becomes clear that her love is never going to be returned. Mopsa is also in unrequited love with Dorus but she is not driven to quite such lengths because of it.
Jealousy
There is a great deal of jealousy in the novella and it always seems to lead to something threatening. For example, Gynecia is extremely jealous of Pyrocles, not only because he refuses to reciprocate her ardor but because her husband seems more interested in Cleophila than he does in his wife. This causes her to become jealous on two counts and prompts her spiral into murderousness. Mopsa's mother is also very jealous and as soon as it is suggested that Dametas might be having an affair with a woman in the neighboring village she hurries there, jealous, which leads to her abandoning her post looking after Pamela and enables Pamela to elope with Midorus. Pamela has also suffered some jealousy when Dorus' wooing of Mopsa becomes a little bit too convincing. Jealousy is both an emotion that is controlling the people feeling it and the catalyst for the tragic events that unfold in the novel.
Political Unrest
The theme of political unrest is never far below the surface of the novella, being mentioned in each of the books, and it is seen as a great accomplishment that Arcadia has not been under threat before since kingdoms all over the globe are falling to invaders. Basilius has been a very popular ruler but by heading into a self imposed exile he is opening the door for detractors to harness the feelings of the citizens who feel that he has betrayed their loyalty by leaving. It seems easy to harness a rabble and to make it errupt. It is shown that his kingdom has been threatened from other nations before and this is one of the factors that he was scared of in the prediction.
Science versus Philosophy
Traditionally, great store had been set by the words and advice of philosophers and the majority of monarchs employed the services of a sooth sayer or an Oracle. Basilius also consults an Oracle but his rejection of the certainty of the prediction he receives shows that he too has begun to set more store in science and logic than in philosophy and spiritual faith. He believes the prediction is accurate, but he also fights it with logic and scientific leanings; if he moves somewhere else and puts his family out of the way of the things that threaten it then he can avoid what is written for him already and rewrite his future the way that he wants it. Moving to B to avoid A is a logical thought process and this demonstrates the way in which the word of logic and science was starting to be given equal credence to previously held beliefs and philosophies.