A hedge fund advisor who is also a priest and his investment advisory firm illegally profited from a scheme to drive down the price of San Diego-based Ligand Pharmaceuticals Inc., reaping more than $1.3 million for the advisor and the hedge fund, the Securities and Exchange Commission charged in a complaint released Wednesday.

According to the complaint, Gregory Lemelson and Massachusetts-based Lemelson Capital Management LLC put out false information about Ligand after Lemelson took a short position in the company in May 2014 on behalf of The Amvona Fund, a hedge fund he advised and partly owned. Short-sellers, the SEC noted, profit when the price of stock declines.

Gregory Lemelson is also known as Father Emmanuel Lemelson, a Greek Orthodox priest, the name he uses on the firm’s website where he is listed as chief investment officer.

The SEC complaint, filed in federal court in Massachusetts, said Ligand’s stock lost more than a third of its value during the course of Lemelson’s alleged scheme.

It said that after taking a short position in the company, Lemelson made false statements in order to undermine investor confidence in the pharmaceutical company, lower its stock price and increase the value of his position. He did this, the complaint charged, by using written reports, interviews and social media to spread untrue claims.

The falsehoods, the SEC said, included that Ligand was “teetering on the brink of bankruptcy” and that the company’s investor relations firm agreed with Lemelson’s view that its flagship Hepatitis C drug, Promacta, was going to become obsolete.

Lemelson also allegedly misled investors by citing a European doctor’s negative views on Promacta. However, he did not reveal that the doctor was Amvona’s largest investor, and had a significant financial interest in seeing Ligand’s stock price decline.

“While short-sellers are free to express their opinions about particular companies, they may not bolster those opinions with false statements, which is what we allege Lemelson did here,” David Becker, an assistant director in the SEC’s Division of Enforcement, said in a statement.

The SEC’s complaint charges Lemelson and Lemelson Capital Management with fraud and seeks to have them return allegedly ill-gotten gains with interest and pay monetary penalties.

The complaint names the Amvona Fund as a relief defendant and seeks to have it return gains it obtained as a result of Lemelson and his firm’s alleged misconduct.

In October 2014, BarclayHedge, a hedge fund database, proclaimed the Amvona Fund the world’s top-performing “long bias” fund for the previous August — which Lemelson proudly trumpeted in a news release.

A year later, media reports were raising questions about how good he really was.