Lyme disease is a tick-borne infection caused by Borrelia burgdorferi, B. garinii, and B. afzelii. These spirochetes experience environmental fluctuations as they are passed between mammalian and Ixodes tick hosts throughout their enzootic cycle. Recent studies have suggested cyclic diguanylate (c-di-GMP), a ubiquitous secondary messenger, is a key modulator of B. burgdorferi adaptive responses and may play a significant role in cycle progression. In this study, we examined the impact of the sole diguanylate cyclase (Rrp1), c-di-GMP binding proteins (PlzA and PlzB), and HD-GYP-containing phosphodiesterase (PdeB) in disease establishment of both murine and Ixodes tick systems. Strains harboring targeted gene deletions or plasmid-based constitutive gene expression constructs were generated. Rrp1 was required for tick colonization, yet overexpression abolished murine disease, thus implicating the requirement of finely regulated c-di-GMP levels for enzootic cycle progression. Deletion of rrp1 disrupted translational motion and swarming patterns by causing extended cell runs, eliminating stops/flexes, and reducing swarming capabilities. This was attributed to a defect in N-acetyl-D-glucosamine (NAG) metabolism and chemotaxis. NAG is a major source of nutrition for B. burgdorferi within the tick environment; therefore this defect would impede spirochete migration towards feeding ticks, as well as pathogen uptake and survival within the Ixodes vector. In contrast, the downstream c-di-GMP effector, PlzA, was critical for murine disease but nonessential for survival within ticks nor functionally complemented by PlzB. Deletion of plzA altered strain motility and swarming similarly to the rrp1 deletion mutant, yet had a distinct phenotype with significantly slower translational motion and no affect on NAG chemotaxis and metabolism. This indicates B. burgdorferi could possess alternate c-di-GMP effectors or Rrp1 could be directly influencing these cellular processes. Uniquely, PdeB did not abolish murine infection via needle inoculation, but wasrequired for natural transmission from ticks. This defect was linked to the decreased tick colonization efficiency upon pdeB deletion. Together, these analyses indicate that c-di-GMP signaling is an important virulence mechanism of Borrelia burgdorferi and demonstrate the complexity of this signaling pathway in an arthropod-borne pathogen. The data presented here additionally provide significant new insight into the gene regulatory mechanisms of the Lyme disease spirochetes.