The class of shuffle ideals is a fundamental sub-family of regular languages. The shuffle ideal generated by a string set $U$ is the collection of all strings containing some string $u \in U$ as a (not necessarily contiguous) subsequence. In spite of its apparent simplicity, the problem of learning a shuffle ideal from given data is known to be computationally intractable. In this paper, we study the PAC learnability of shuffle ideals and present positive results on this learning problem under element-wise independent and identical distributions and Markovian distributions in the statistical query model. A constrained generalization to learning shuffle ideals under product distributions is also provided. In the empirical direction, we propose a heuristic algorithm for learning shuffle ideals from given labeled strings under general unrestricted distributions. Experiments demonstrate the advantage for both efficiency and accuracy of our algorithm.