This work investigates whether the reproductive performance of Mediterranean goats achieved using melatonin implants at around the spring equinox is affected by the protocol followed, i.e. implanting females only, males only, both sexes or neither sex. In a first experiment, Murciano-Granadina females (n = 419, 510 and 631 for three consecutive years) were divided into four groups: treated with melatonin (FM) and not treated with melatonin (FC), mounted by males treated with melatonin (MM) or not (MC). In a second experiment, performed during 2009, the same protocols were used with 635 Payoya females and the results compared with those obtained for the same year for the Murciano-Granadina breed. Fertility (percentage of goats kidding), litter size (number of kids born per female kidded) and productivity (number of kids per female in each mating group) were calculated. In the first experiment, better reproductive performances were obtained when females (overall fertility: 71.1% vs 57.0% for the FM and FC animals; productivity 1.37 ± 0.04 kids per female vs 1.12 ± 0.03 kids per female for the FM and FC animals; p < 0.01) or males (overall fertility: 65.9% vs 58.4 for the MM and MC animals; productivity 1.28 ± 0.03 kids per female vs 1.13 ± 0.04 kids per female for MM and MC groups, respectively; p < 0.01) were implanted with melatonin. Moreover, the interaction sex × melatonin treatment had a significant effect (p < 0.05) on productivity. In the second experiment, for the Murciano-Granadina breed, the greatest increase in the number of kids born per female was obtained when the females were treated with melatonin, in either the FM/MC or FM/MM protocols (0.54 extra kids and 0.53 extra kids per female, respectively) (p < 0.01). In the Payoya breed, the greatest increase was obtained using the FM/MC protocol (0.19 extra kids per female). Thus, improved reproductive performances are obtained when female Murciano-Granadina and Payoya goats are implanted with melatonin, although important differences in reproductive performance are seen between the breeds.