In this new text, designed for sophomores studying mathematics and computer science, the authors cover the basics of difference equations and some of their applications in computing and in population biology. Each chapter leads to techniques that can be applied by hand to small examples or programmed for larger problems. Along the way, the reader will use linear algebra and graph theory, develop formal power series, solve combinatorial problems, visit Perron--Frobenius theory, discuss pseudorandom number generation and integer factorization, and apply the Fast Fourier Transform to multiply polynomials quickly. The book contains many worked examples and over 250 exercises. While these exercises are accessible to students and have been class-tested, they also suggest further problems and possible research topics.