A resident of the 700 block of Crinella Drive called police around 12:10 a.m. after arriving home to find the suspect inside the residence, police said.
The 6-foot-tall suspect allegedly pointed the gun at the man, threatened him and told him to leave.
The resident was eventually able to call police, who arrived within two minutes of the phone call but were unable to locate the suspect.
The resident told police someone had gone through his belongings but the plants were the only things missing. The suspect had apparently broken the plants at the base, put them into white trash bags and fled, police said.
Police did not find any signs of forced entry.
The case is under investigation and anyone with information is asked to call the Petaluma Police Department at (707) 778-4372.