The snake pipefish, Entelurus aequoreus, is a widespread marine species occurring in pelagic and coastal environments in the northeastern Atlantic Ocean. Recently, the snake pipefish underwent a short-lived, yet substantial, increase in abundance and range expansion into arctic waters. However, little is known about the species’ population structure or if different ecotypes contributed to this outbreak. Specimens (n=178) were sampled from 25 locations from six regions spanning 1.9 million km2. A fragment of the mitochondrial cytochrome b gene and control region was used to assess population structure and genetic diversity. Both loci showed high haplotype diversity (Hd) and low nucleotide diversity (π) over all sampled locations. A genetic signature of population expansion was evident through mismatch distributions and tests for recent population expansion (Fu’s Fs, Tajima’s D, and R2). Effective population size analyses (Bayesian Skyline Plot) suggest an ancient expansion (50-100 thousand years ago). However, we found neither significant population differentiation (AMOVA) among regions, nor evidence of genetically distinct ecotypes. This lack of structure is likely due to a pelagic life style, fast development and long distance dispersal aided by ocean currents. Our work highlights the need for further research to better understand the recent outbreak and how this species may respond to future environmental challenges.