Fitness is the ultimate measure of organismal function; however, technical challenges can limit researchers' ability to quantify fitness. We developed a simple and inexpensive method of marking eggs inside of the ovary of a nesting fish, the bluebanded goby (Lythrypnus dalli), in order to quantify female reproductive success. Multiple females in a harem of L. dalli can lay eggs inside of the male's nest within a short period of time, making the timing of egg laying or developmental stage of the eggs insufficient to identify which female laid which clutch of eggs. After injecting small volumes of food coloring into the ovaries, each female's eggs can be identified throughout development by the color of the yolk. We make preliminary observations about the efficacy of different colors (red, yellow, green, blue) for use in L. dalli, including effects on female survival, social behavior, and the enzyme immunoassays used to quantify hormones. While rigorous validations should be conducted for each species and experimental context, this method of marking eggs has the potential to be broadly useful for directly estimating fitness in species with external fertilization, thus facilitating research in reproductive biology, behavioral ecology, and evolution.