It is the first time a black rhino, which is listed among endangered species, has been killed inside the protected area.
Kenya Wildlife Service (KWS) senior warden in charge of Narok Tuqa Jirmo said the death of the rhino whose horns were removed by the poachers was unnatural.
Mr Jirmo said poaching of rhinos and elephants inside and out of the reserve had in the last three months gone up.
He said: “The trend in Mara and elsewhere in the country shows poaching of rhinos and elephants has gone up and if nothing is going to be done, their population will dwindle”.
Security personnel cordoned off the area and it was not immediately established whether the poachers killed the rhino using a gun.
The incident happened despite the presence of a well-funded Rhino Surveillance Unit in the reserve.
In the 1980s when poaching was rampant, the population of rhinos and elephants in the country went down from about 3,000 to below 400 for rhinos while elephant dwindled from 150,000 to 15,000.
Population of black rhinos in Mara has now gone down from 38 to 37.
Siana Wildlife Conservation Trust manager Samuel Nkoitoi said poaching activities in Mara bode ill for conservation efforts, adding surveillance efforts need to be enhanced.
Tuqa added that due to the proximity to Tanzania and the vastness of the area, the poachers could have crossed the common border to kill the rhino.
He said investigations into the incident by a team of KWS and county council officials have been launched.
Elsewhere, KWS officers have arrested three suspected poachers and recovered five tusks as the war against poaching activities in Tsavo National Park intensified.
The intelligence team intercepted the poachers with ivory weighing 29kg at Kone in northern part of the park.
KWS said the arrest brings to 10 the number of poachers so far arrested and four elephants killed in the park in the past one month.
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