Thoroughly soak the rockwool cubes in water. Drain the cubes and place one jalapeno seed in each cube. Place the cubes on a planting tray.
Cover the tray with the lid. Place the tray in indirect sunlight, where it's warm. Peppers germinate best when the air temperature is between 68 and 70 degrees F.
Check the seeds daily. Remove the tray lid and look at the progress of the seeds. If the cubes seem dry, mist them with water. Removing the lid also gives the seeds fresh air.
Remove the tray lid completely when the jalapeno seeds start to sprout. Keep the cubes moist by spraying them with water. When they are 2 to 3 inches tall, they're ready for the next hydroponic phase.
Assemble the hydroponic nutrient system and tank. This can be in a darker place that has an even temperature. Basements are good locations. Place the rockwool cubes with the seedlings attached into the tank. The jalapeno seedlings need to be about 14 inches apart to give them plenty of room for growth.
Set the grow light up so that it's 3 to 4 inches above your plants. You will need to adjust the light as the plants grow. The light needs to stay on for 14 to 16 hours per day.
Pollinate your plants. When flowers appear, take a dry paintbrush and lightly brush it against the flowers from plant to plant.
Harvest peppers as they ripen. This not only gives you a ready supply of jalapenos, but it also encourages new growth.