Data set of the research paper: Temporal and interspecific dietary variation in wintering ducks in agricultural landscapes Haruko Ando1, Susumu Ikeno2, Ayu Narita3, Taketo Komura4, Atsushi Takada5, Yuji Isagi6, Hiroyuki Oguma1, Tomomi Inoue1, Akio Takenaka1 1 Biology Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan. 2 Wild Bird Society of Japan Ibaraki, 1-4-10 Hakamaduka, Mito, Ibaraki, 310-0055, Japan. 3Forestry Research Institute, Hokkaido Research Organization, Higashiyama, Koushunai-cho, Bibai, Hokkaido, 079-0198, Japan. 4 IDEA Consultants, Inc., Tuzuki-ku, Yokohama, Kanagawa, 224-0025, Japan. 5 Nara Prefectural Government, Noborioji-cho, Nara, 630-8501, Japan 6Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan. Contact: ando.haruko@nies.go.jp Year of data collection: 2015-2017 Location: Ibaraki prefecture, Japan Data description: FASTQ files of fecal DNA sequences for plant and invertebrate diet, the FASTA files for bird and plant species identification, sample information, original plant and invertebrate diet data for each sample Sample info.xlsx: General information and mitochondrial 12S sequences of bird species for each fecal sample Duck_invertebrate.zip: FASTQ files of invertebrate mitochondrial CO1 sequence reads from fecal samples of dabbling ducks. Duck_plant.zip: FASTQ files of plant chloroplast trnL P6loop sequence reads from fecal samples of dabbling ducks. Kasumi_birds_12S.fas: Reference sequences for bird identification of fecal samples Kasumi_plants_P6loop.fas: Reference sequences for plant food identification detected from fecal samples Plant_fa_duck.csv: Plant sequence composition in family level of each fecal sample after rarefaction Plant_sp_duck.csv: Plant sequence composition in the lowest taxonomic level of each fecal sample after rarefaction Animal_fa_duck.csv: Invertebrate sequence composition in family level of each fecal sample after rarefaction