Darkness rarely lasted long in the skies over Lake Maracaibo. An hour after dusk the show would begin: a lightning bolt, then another, and another, until the whole horizon flashed white.

Electrical storms, product of a unique meteorological phenomenon, have lit up nights in this corner of Venezuela for thousands of years. Francis Drake abandoned a sneak attack on the city of Maracaibo in 1595 when lightning betrayed his ships to the Spanish garrison.

But now the lightning has vanished. A phenomenon that once unleashed up to 20,000 bolts a night stopped in late January. Not a single bolt has been seen since.

"This is unprecedented. In recorded history we have not had such a long stretch without lightning," said Erik Quiroga, an environmentalist and leading authority on the Relampago de Catatumbo, or Catatumbo Lightning.

The spectacle, one of the longest single displays of continuous lightning in the world, lasts up to nine hours a night. On average it is visible over 160 nights a year and from 400km away. Lightning bolts discharged from cloud to cloud strike 16 to 40 times a minute. They can reach an intensity of 400,000 amps but are so high thunder is inaudible. There are similar phenomena in Colombia, Indonesia and Uganda but they do not last the whole night.

Fishermen in the village of Congo Mirador, a collection of wooden huts on stilts at the phenomenon's epicentre, are puzzled and anxious by its absence. "It has always been with us," said Edin Hernandez, 62. "It guides us at night, like a lighthouse. We miss it."

The celestial spectacular appears to be a casualty of the El Niño weather phenomenon, which has disrupted global weather patterns and caused a severe drought in Venezuela. Rain has all but disappeared, drying up rivers and disrupting the conditions that produce the lightning, whose causes remain unclear. One theory links it to decomposing organic materials which release methane. Another links it to Andean winds blowing across marshes, generating low pressure and building up an electrical charge in the atmosphere.

The last time the phenomenon vanished was in 1906 after a catastrophic 8.8-magnitude earthquake off the coast of Ecuador and Colombia unleashed a tsunami. The lightning returned three weeks later.

Now it is five weeks and there is still no sign of the nocturnal flashes.

"I look for it every night but there is nothing," said Francisca Hernandez, 28, a schoolteacher in Congo Mirador who monitors Lake Maracaibo's sky for researchers based in Caracas.

Some scientists believe the electrical storms help replenish the ozone layer. Others doubt that, saying the ozone they produce reaches only the tropospheric atmosphere.

The drought has also extinguished many man-made lights across Venezuela as the country relies largely on hydropower. Last month, the president, Hugo Chávez, declared an electricity emergency and said severe rationing, which has blacked out towns and cities, could last months. One state electricity company told workers to pray for rain.

Losing the lightning is a symbolic blow. In addition to warding off Drake's naval assault – an event celebrated in Lope de Vega's 1598 epic poem – it is credited with helping independence fighters defeat a Spanish fleet in 1823. The state of Zulia, which encompasses Lake Maracaibo, has a lightning bolt across its centre and refers to the phenomenon in its anthem.

Quiroga worries that when rains return the lightning may not recover its former glory. It was dwindling in frequency and force even before the drought, probably because deforestation and agriculture had clogged the Catatumbo river and several lagoons with silt.

"This is a unique gift and we are at risk of losing it," said Quiroga, who has led scientific teams to its epicentre. He has lobbied Venezuelan authorities to protect the area and the United Nations to recognise it as a world heritage site. A Unesco spokeswoman said there were no plans to do so because electrical storms did not have a "site".