In this experiment Syngnathus typhle individuals were collected at six different locations along the German Baltic Sea coastline. To analyse the populations structure of the pipefish we isolated genomic DNA from fin clips of collected pipefish female. All 144 female S. typhle samples were genotyped for 11 microsatellite loci, with a minimum of 20 individuals per sampling site. The allele report contains the microsatelite length of the three primer pools used for multiplex PCR. The report gives information, if indivuduals are homozygous (same allele length) or heterozygous (different allele length) for targeted alleles. Some samples were negelected due to too many missing alleles. Allele reports were uploaded in Microchecker and Genetix for analyses of the population structure.