AbstractAngiosperms have co‐evolved with animals over thousands of years leading to an array of mutualistic relationships. Passage of plant seeds through animal intestines leads to an important mutualism providing the animal with food and the plant with seed dispersal and enhanced germination. This phenomenon is well studied in terrestrial angiosperms, but there is less research in aquatic environments. We studied the effect of gut passage in marine mega‐herbivores (green sea turtles and dugongs) on seed germination for a common Australian seagrass, Zostera muelleri.We collected fecal samples likely to contain seeds, as well as seagrass seeds from plants at two coastal seagrass meadows in the central Great Barrier Reef World Heritage Area, Australia. Seeds collected from feces and plants were subjected to germination trials across different temperature treatments: low (19°C), medium (26°C), and high (32°C). We found excreted seeds had a significantly greater germination probability (two to four times greater) and germinated significantly faster (18–61% faster) than seeds from the plant. Excreted seeds which had not germinated at the end of the experiment were significantly less likely to be viable compared with seeds taken from the plant. Seeds released from the plant have a slow germination and low germination probability compared with excreted seeds, but retain a high percentage of seed viability. Our study is the first record of marine mega‐herbivores enhancing germination of Z. muelleri seeds. By transporting seeds to new locations and enhancing germination, these animals are important in seagrass resilience and connectivity among metapopulations.