Crowther's trades were legitimate and Pushpay was not the subject of the investigation, the FMA said.
The matter was referred to FMA by stock market regulator NZ RegCo (formerly known as NZX Regulation) in July 2018.
One individual faces a criminal charge, which had been filed in the Auckland District Court, and both individuals would face civil proceedings in the Auckland High Court.
The individuals have been granted interim name suppression until their first court appearance.
It was just the fourth insider trading case the FMA had encountered.
Insider trading involves the buying and selling of shares in a listed company by someone with access to material information about the firm that has not been made public.
"Unethical trading activity can undermine market integrity and erode investor confidence at a fundamental level," the FMA said.
Criminal insider trading carries a punishment of up to five years in prison or a maximum fine of $500,000.
Civil penalties could include a pecuniary penalty not exceeding the greatest of the consideration for the relevant transaction, three times the amount of the gain made or the loss avoided, as $1m in the case of an individual or $5m in any other case.
Pushpay chairman Graham Shaw said it had co-operated with the FMA's investigation and supported its commitment to the integrity of the capital markets.
Shaw said the company had robust policies in place at all relevant times.
"We take seriously our responsibilities as a listed company, and our values, ethics and integrity as a company are at the heart of our business practices."
