We consider random subgroups of Thompson's group F with respect to two natural stratifications of the set of all k generator subgroups. We find that the isomorphism classes of subgroups which occur with positive density are not the same for the two stratifications. We give the first known examples of persistent subgroups, whose isomorphism classes occur with positive density within the set of k-generator subgroups, for all sufficiently large k. * The first, second and fourth authors received support from a Bowdoin College Faculty Research Award. The first author acknowledges support from a PSC-CUNY Research Award. The second author acknowledges the support of the Algebraic Cryptography Center at Stevens Institute of Technology, Hoboken New Jersey during the writing of this article. The third author thanks NSERC of Canada for financial support. The fourth author acknowledges support from NSF grant DMS-0604645.† Corresponding author 1 Additionally, Thompson's group provides the first example of a group without a generic isomorphism class of subgroup. Elements of F are represented uniquely by reduced pairs of finite rooted binary trees. We compute the asymptotic growth rate and a generating function for the number of reduced pairs of trees, which we show is D-finite and not algebraic. We then use the asymptotic growth to prove our density results.